Note: Descriptions are shown in the official language in which they were submitted.
METHODS FOR GENDER ASSEMBLY AND HAPLOTYPE PHASING
[0001]
TECHNICAL FIELD
(0002] The disclosure provides for methods of genome assembly
and haplotype phasing for identifying short, intermediate and long
term connections within a genome.
BACKGROUND
[0003] It remains difficult in theory and in practice to
produce high-quality, highly contiguous genome sequences.
SUMMARY
[0004] A persistent shortcoming of next generation sequencing
(NGS) data is the inability to span large repetitive regions of
genomes due to short read lengths and relatively small insert
sizes. This deficiency significantly affects de nova assembly.
Contigs separated by long repetitive regions cannot be linked or
re-sequenced, since the nature and placement of genomic
rearrangements are uncertain. Further, since variants cannot be
confidently associated with haplotypes over long-distances, phasing
information is indeterminable. The disclosure can address all of
these problems simultaneously by generating extremely long-range
read pairs (XLRPs) that span genomic distances on the order of
hundreds of kilobases, and up to megabases with the appropriate
input DNA. Such data can be invaluable for overcoming the
substantial barriers presented by large repetitive regions in
genomes, including centromeres; enable cost-effective de nova
assembly; and produce re-sequencing data of sufficient integrity
and accuracy for personalized medicine.
[0005] Of significant importance is the use of reconstituted
chromatin in forming associations among very distant, but
molecularly-linked, segments of DNA. The disclosure enables
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distant segments to be brought together and covalently linked by
chromatin conformation, thereby physically connecting previously
distant portions of the DNA molecule. Subsequent processing can
allow for the sequence of the associated segments to be
ascertained, yielding read pairs whose separation on the genome
extends up to the full length of the inpuL DNA molecules. Since
the read pairs are derived from the same molecule, these pairs also
contain phase information.
[0006] In some embodiments, the disclosure provides methods
that can produce high quality assemblies with far less data than
previously required. For example, the methods disclosed herein
provide for genomic assembly from only two lanes of Illumine HiSeq
data.
[0007] In other embodiments, the disclosure provides methods
that can generate chromosome-level phasing using a long-distance
read pair approach. For example, the methods disclosed herein can
phase 90% or more of the heterozygous single nucleotide
polymorphisms (SNPs) for that individual to an accuracy of at least
99'f% or greater. This accuracy Is on par with phasing produced by
substantially more costly and laborious methods.
[0008] In some examples, methods that can produce fragments of
genomic DNA up to megabase scale can be used with the methods
disclosed herein. Long DNA fragments can be generated to confirm
the ability of the present methods to generate read pairs spanning
the longest fragments offered by those extractions. In some cases,
DNA fragments beyond 150 kbp in length can be extracted and used to
generate XLRP libraries.
[0009] The disclosure provides methods for greatly accelerating
and improving de novo genome assembly. The methods disclosed herein
utilize methods for data analysis that allow for rapid and
inexpensive de novo assembly of genomes from one or more subjects.
The disclosure further provides that the methods disclosed herein
can be used in a variety of applications, including haplotype
phasing, and metagenomics analysis.
[0010] In certain embodiments, the disclosure provides for a
method for genome assembly comprising the steps of: generating a
plurality of contigs; generating a plurality of read pairs from
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data produced by probing the physical layout of chromosomes,
chromatin, or reconstituted chromatin; mapping or assembling the
plurality of read pairs to the plurality of contigs; constructing
an adjacency matrix of contigs using the read-mapping or assembly
data; and analyzing the adjacency matrix to determine a path
through the contigs that represent their order and/or orientation
to the genome. In further embodiments, the disclosure provides
that at least about 90% of the read pairs are weighted by taking a
function of each read's distance to the edge of the contig so as to
incorporate information about which read pairs indicate short-range
contacts and which read pairs indicate longer-range contacts. In
other embodiments, the adjacency matrix can be re-scaled to down-
weight the high number of contacts on some contigs that represent
promiscuous regions of the genome, such as conserved binding sites
for one or more agents that regulate the scaffolding interactions
of chromatin, like transcriptional repressor CTCF. In other
embodiments, the disclosure provides for a method for the genome
assembly of a human subject, whereby the plurality of contigs is
generated from the human subject's DNA, and whereby the plurality
of read pairs is generated from analyzing the human subject's
chromosomes, chromatin, or reconstituted chromatin made from the
subject's naked DNA.
[0011] In further embodiments, the disclosure provides that a
plurality of contigs can be generated by using a shotgun sequencing
method comprising: fragmenting long stretches of a subject's DNA
into random fragments of indeterminate size; sequencing the
fragments using high throughput sequencing methods to generate a
plurality of sequencing reads; and assembling the sequencing reads
so as to form a plurality of contigs.
[0012] In certain embodiments, the disclosure provides that a
plurality of read pairs can be generated by probing the physical
layout of chromosomes, chromatin, or reconstituted chromatin using
a Hi-C based technique. In further embodiments, the Hi-C based
technique comprises, crosslinking chromosomes, chromatin, or
reconstituted chromatin with a fixative agent, such as
formaldehyde, to form DNA-protein cross links; cutting the cross-
linked DNA-Protein with one or more restriction enzymes so as to
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generate a plurality of DNA-protein complexes comprising sticky
ends; filling in the sticky ends with nucleotides containing one or
more markers, such as biotin, to create blunt ends that are then
ligated together; fragmenting the plurality of DNA-protein
complexes into fragments; pulling down junction containing
fragments by using the one or more of the markers; and sequencing
the junction containing fragments using high throughput sequencing
methods to generate a plurality of read pairs. In further
embodiments, the plurality of read pairs for the methods disclosed
herein is generated from data produced by probing the physical
layout of reconstituted chromatin.
[0013] In various embodiments, the disclosure provides that a
plurality of read pairs can be determined by probing the physical
Layout of chromosomes or chromatin isolated from cultured cells or
primary tissue. In other embodiments, the plurality of read pairs
can be determined by probing the physical layout of reconstituted
chromatin formed by complexing naked DNA obtained from a sample of
one or more subjects with isolated histones.
[0014] In other embodiments, the disclosure provides a method
to determine haplotype phasing comprising a step of identifying one
or more sites of heterozygosity in the plurality of read pairs,
wherein phasing data for allelic variants can be determined by
identifying read pairs that comprise a pair of heterozygous sites.
[0015] In various embodiments, the disclosure provides a method
for high-throughput bacterial genome assembly, comprising a step of
generating a plurality of read pairs by probing the physical layout
of a plurality of microbial chromosomes using a modified Hi-C based
method, comprising the modified steps of: collecting microbes from
an environment; adding a fixative agent, such as formaldehyde, so
as to form cross-links within each microbial cell, and wherein read
pairs mapping to different contigs indicate which contigs are from
the same species.
[0016] In some embodiments, the disclosure provides a method
for genome assembly comprising: (a) generating a plurality of
contigs; (b) determining a plurality of read pairs from data
generated by probing the physical layout of chromosomes, chromatin,
or reconstituted chromatin; (c) mapping the plurality of read pairs
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to the plurality of contigs; (d) constructing an adjacency matrix
of contigs using the read-mapping data; and (e) analyzing the
adjacency matrix to determine a path through the contigs that
represent their order and/or orientation to the genome.
[0017] In further embodiments, the disclosure provides a method
to generate a plurality of read pairs by probing the physical
layout of chromosomes, chromatin, or reconstituted chromatin using
a Hi-C based technique. In further embodiments, the Hi-C based
technique comprises (a) crosslinking chromosomes, chromatin, or
reconstituted chromatin with a fixative agent to form DNA-protein
cross links; (b) cutting the crosslinked DNA-Protein with one or
more restriction enzymes so as to generate a plurality of DNA-
protein complexes comprising sticky ends; (c) filling in the sticky
ends with nucleotides containing one or more markers to create
blunt ends that are then ligated together; (d) shearing the
plurality of DNA-protein complexes into fragments; (e) pulling down
junction containing fragments by using one or more of the markers;
and (f) sequencing the junction containing fragments using high
throughput sequencing methods to generate a plurality of read
pairs.
[0018] In certain embodiments, the plurality of read pairs is
determined by probing the physical layout of chromosomes or
chromatin isolated from cultured cells or primary tissue. In other
embodiments, the plurality of read pairs is determined by probing
the physical layout of reconstituted chromatin formed by complexing
naked DNA obtained from a sample of one or more subjects with
isolated histones.
[0019] In some embodiments, at least about 50%, about 60%,
about 70%, about 80%, about 90%, about 95% or about 99% or more of
the plurality of read pairs are weighted by taking a function of
the read's distance to the edge of the contig so as to incorporate
a higher probability of shorter contacts than longer contacts. In
some embodiments, the adjacency matrix is re-scaled to down-weight
the high number of contacts on some contigs that represent
promiscuous regions of the genome.
[0020] In certain embodiments, the promiscuous regions of the
genome include one or more conserved binding sites for one or more
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agents that regulate the scaffolding interactions of chromatin. In
some examples, the agent is transcriptional repressor CTCF.
[0021] In some embodiments, the methods disclosed herein
provide for the genome assembly of a human subject, whereby the
plurality of contigs is generated from the human subject's DNA, and
whereby the plurality of read pairs is generated from analyzing the
human subject's chromosomes, chromatin, or reconstituted chromatin
made from the subject's naked DNA.
[0022] In other embodiments, the disclosure provides a method
for determining haplotype phasing, comprising identifying one or
more sites of heterozygosity in the plurality of read pairs,
wherein phasing data for allelic variants can be determined by
identifying read pairs that comprise a pair of heterozygous sites.
[0023] In yet other embodiments, the disclosure provides a
method for meta-genomics assemblies, wherein the plurality of read
pairs is generated by probing the physical layout of a plurality of
microbial chromosomes using a modified Hi-C based method,
comprising: collecting microbes from an environment; and adding a
fixative agent so as to form cross-links within each microbial
cell, and wherein read pairs mapping to different contigs indicate
which contigs are from the same species. In some examples, the
fixative agent is formaldehyde.
[0024] In some embodiments, the disclosure provides a method of
assembling a plurality of contigs originating from a single DNA
molecule, comprising generating a plurality of read-pairs from the
single DNA molecule and assembling the contigs using the read-
pairs, wherein at least 1% of the read-pairs span a distance
greater than 50 kB on the single DNA molecule and the read-pairs
are generated within 14 days. In some embodiments, at least 10% of
the read-pairs span a distance greater than 50 kB on the single DNA
molecule. In other embodiments, at least JA of the read-pairs span
a distance greater than 100 kB on the single DNA molecule. In
further embodiments, the read-pairs are generated within 7 days.
[0025] In other embodiments, the disclosure provides a method
of assembling a plurality of contigs originating from a single DNA
molecule, comprising generating a plurality of read-pairs from the
single DNA molecule in vitro and assembling the contigs using the
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read-pairs, wherein at least 1% of the read-pairs span a distance
greater than 30 kB on the single DNA molecule. In some embodiments,
at least 10% of the read-pairs span a distance greater than 30 kB
on the single DNA molecule. In other embodiments, at least 1% of
the read-pairs span a distance greater than 50 kB on the single DNA
molecule.
[0026] In yet other embodiments, the disclosure provides a
method of haplotype phasing, comprising generating a plurality of
read-pairs from a single DNA molecule and assembling a plurality of
contigs of the DNA molecule using the read-pairs, wherein at least
1% of the read-pairs spans a distance greater than 50 kB on the
single DNA molecule and the haplotype phasing is performed at
greater than 70% accuracy. In some embodiments, at least 10% of the
read-pairs span a distance greater than 50 kB on the single DNA
molecule. In other embodiments, wherein at least 1% of the read-
pairs span a distance greater than 100 kB on the single DNA
molecule. In further embodiments, the haplotype phasing is
performed at greater than 90% accuracy.
[0027] In further embodiments, the disclosure provides a method
of haplotype phasing, comprising generating a plurality of read-
pairs from a single DNA molecule in vitro and assembling a
plurality of contigs of the DNA molecule using the read-pairs,
wherein at least Ds of the read-pairs spans a distance greater than
30 kB on the single DNA molecule and the haplotype phasing is
performed at greater than 70% accuracy. In some embodiments, at
least 10% of the read-pairs span a distance greater than 30 kB on
the single DNA molecule. In other embodiments, at least 1% of the
read-pairs span a distance greater than 50 kB on the single DNA
molecule. In yet other embodiments, the haplotype phasing is
performed at greater than 90% accuracy. In further embodiments, the
haplotype phasing is performed at greater than 70% accuracy.
[0028] In some embodiments, the disclosure provides a method of
generating a first read-pair from a first DNA molecule, comprising:
(a) crosslinking the first DNA molecule in vitro, wherein the first
DNA molecule comprises a first DNA segment and a second DNA
segment; (b) linking the first DNA segment with the second DNA
segment and thereby forming a linked DNA segment; and (c)
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sequencing the linked DNA segment and thereby obtaining the first
read-pair.
[0029] In some embodiments, a plurality of association
molecules, such as from reconstituted chromatin, are cross-linked
to the first DNA molecule. In some examples, the association
molecules comprise amino acids. In further examples, the
association molecules are peptides or proteins. In certain
embodiments, the first DNA molecule is cross-linked with a fixative
agent. In some examples, the fixative agent is formaldehyde. In
some embodiments, the first DNA segment and the second DNA segment
are generated by severing the first DNA molecule. In certain
embodiments, the method further comprises assembling a plurality of
contigs of the first DNA molecule using the first read-pair. In
some embodiments, each of the first and the second DNA segment is
connected to at least one affinity label and the linked DNA segment
is captured using the affinity label.
[0030] In further embodiments, the method further comprises:
(a) providing a plurality of association molecules, such as from
reconstituted chromatin, to at least a second DNA molecule; (b)
crosslinking the association molecules to the second DNA molecule
and thereby forming a second complex in vitro; (c) severing the
second complex thereby generating a third DNA segment and a fourth
segment; (d) linking the third DNA segment with the fourth DNA
segment and thereby forming a second linked DNA segment; and (e)
sequencing the second linked DNA segment and thereby obtaining a
second read-pair. In some examples, less than 40% of the DNA
segments from the DNA molecules are linked with DNA segments from
any other DNA molecule. In further examples, less than 20% of the
DNA segments from the DNA molecules are linked with DNA segments
from any other DNA molecule.
[0031] In other embodiments, the disclosure provides a method
of generating a first read-pair from a first DNA molecule
comprising a predetermined sequence, comprising: (a) providing one
or more DNA-binding molecules to the first DNA molecule, wherein
the one or more DNA-binding molecules bind to the predetermined
sequence; (b) crosslinking the first DNA molecule in vitro, wherein
the first DNA molecule comprises a first DNA segment and a second
Date Recue/Date Received 2023-08-15
DNA segment; (c) linking the first DNA segment with the second DNA
segment and thereby forming a first linked DNA segment; and (d)
sequencing the first linked DNA segment and thereby obtaining the
first read-pair; wherein the probability that the predetermined
sequence appears in the read-pair is affected by the binding of the
DNA-binding molecule to the predetermined sequence.
[0032] In some embodiments, the DNA-binding molecule is a
nucleic acid that can hybridize to the predetermined sequence. In
some examples the nucleic acid is RNA. in other examples, the
nucleic acid is DNA. In other embodiments, the DNA-binding molecule
is a small molecule. In some examples, the small molecule binds to
the predetermined sequence with a binding affinity less than 100
pM. In further examples, the small molecule binds to the
predetermined sequence with a binding affinity less than 1 pM. In
further embodiments, the DNA-binding molecule is immobilized on a
surface or a solid support.
[0033] In some embodiments, the probability that the
predetermined sequence appears in the read-pair is decreased. In
other embodiments, the probability that the predetermined sequence
appears in the read-pair is increased.
[0034] In yet other embodiments, the disclosure provides an in
vitro library comprising a plurality of read-pairs each comprising
at least a first sequence element and a second sequence element,
wherein the first and the second sequence elements originate from a
single DNA molecule and wherein at least 1% of the read-pairs
comprise first and second sequence elements that are at least 50 kB
apart on the single DNA molecule.
[0035] In some embodiments, at least 10% of the read-pairs
comprise first and second sequence elements that are at least 50 kB
apart on the single DNA molecule. In other embodiments, at least 1%
of the read-pairs comprise first and second sequence elements that
are at least 100 kB apart on the single DNA molecule.
[0036] In further embodiments, less than 20% of the read-pairs
comprise one or more predetermined sequences. In further
embodiments, less than 10% of the read-pairs comprise one or more
predetermined sequences. In yet further embodiments, less than 5,4
of the read-pairs comprise one or more predetermined sequences.
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[0037] In some embodiments, the predetermined sequences are
determined by one or more nucleic acids that can hybridize to the
predetermined sequences. In some examples, the one or more nucleic
acids is RNA. In other examples, the one or more nucleic acids is
DNA. In further examples, the one or more nucleic acids is
immobilized to a surface or a solid support.
[0038] In other embodiments, the predetermined sequences are
determined by one or more small molecule. In some examples, the one
or more small molecule binds to the predetermined sequences with a
binding affinity less than 100 pM. In further examples, the one or
more small molecule binds to the predetermined sequences with a
binding affinity less than 1 pM.
[0039] In some embodiments, the disclosure provides a
composition comprising a DNA fragment and a plurality of
association molecules, such as from reconstituted chromatin,
wherein: (a) the association molecules are cross-linked to the DNA
fragment in an in vitro complex; and (b) the in vitro complex is
immobilized on a solid support.
[0040] In other embodiments, the disclosure provides a
composition comprising a DNA fragment, a plurality of association
molecules, and a DNA-binding molecule, wherein: (a) the DNA-binding
molecule is bound to a predetermined sequence of the DNA fragment;
and (b) the association molecules are cross-linked to the DNA
fragment.
[0041] In some embodiments, the DNA-binding molecule is a
nucleic acid that can hybridize to the predetermined sequence. In
some examples, the nucleic acid is RNA. In other examples, the
nucleic acid is DNA. In further examples, the nucleic acid is
immobilized to a surface or a solid support.
[0042] In other embodiments, the DNA-binding molecule is a
small molecule. In some examples, the small molecule binds to the
predetermined sequence with a binding affinity less than 100 pM. In
other examples, the small molecule binds to the predetermined
sequence with a binding affinity less than 1 pM.
[0043]
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BRIEF DESCRIPTION OF THE DRAWINGS
[0044] The novel features of the disclosure are set forth with
particularity in the appended claims. A better understanding of
the features and advantages of the disclosure will be obtained by
reference to the following detailed description that sets forth
illustrative embodiments, in which the principles of the disclosure
are utilized, and the accompanying drawings of which:
[0045] Figure 1 presents an illustration of genome assembly
using high-throughput sequencing reads. The genome to be assembled
is shown (top). Typically, genomes have many repeat sequences that
are difficult to assemble. Random, high-throughput sequence data
from genomes (middle) are collected and assembled into "contigs" in
regions that are unique in the genome (bottom). Contig assembly
generally stops at the many repeat sequences. The final output is a
set of thousands of contigs whose order and orientation relative to
one another are not known. In the figure, they are arbitrarily
numbered from longest to shortest.
[0046] Figure 2A-D illustrates a Hi-C based protocol of the
disclosure: (k) demonstrates where DNA is cross-linked and
processed to created biotinylated junction fragments for
sequencing; and (B-D) provide contact nap data on human chr14 for a
variety of restriction enzymes. As shown, most contacts are local
along the chromosome.
[0047] Figure SA-C provides a method of the disclosure using
Hi-C sequence data to assist genome assembly: (A) illustrates where
DNA is cross-linked and processed using a Hi-C based protocol; (B)
demonstrates where read-pair data is mapped to assembled contigs,
generated from random shotgun sequencing and assembly; and (C)
illustrates that after filtering and weighting, an adjacency matrix
summarizing all inter-contig read pair data can be constructed.
This matrix can be re-ordered to indicate the correct assembly
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path. As shown, most of the read pairs will map within a contig.
From which, it is possible to learn the distribution of contact
distances (e.g., see FIG. 6). Read pairs that map to different
contigs provide data about which contigs are adjacent in a correct
genome assembly.
[0048] Figure 4 illustrates an exemplary protocol of the
disclosure: DNA fragments are first generated and prepared;
followed by in vitro chromatin assembly and biotinylation; the
chromatin/DNA complex is then fixed with formaldehyde and pulled
down with streptavadin beads; the complexes are then restriction
digested to generate sticky ends that are then filled with
biotinylated dCTP and interior, sulfated GTP; following blunt-end
ligation, the chromatin/DNA complex undergoes proteinase digestion,
exonuclease digestion and shearing; after which the DNA fragments
are pulled pulled-down with biotin and ligated with a sequencing
adaptor; and finally, the DNA fragments are selected by size and
sequenced.
[0049] Figure 5A-8 provides an illustration of the ambiguities
that arise in genomic assembly and alignment from repetitive
regions in the genome. (A) Uncertainty in linkage results from read
pairs that cannot bridge repetitive regions. (B) Uncertainty in
placement of segment because read pairs cannot span bordering
repeats.
[0050] Figure 6 illustrates the distribution of genomic
distances between read pairs from a human XLRP library. Maximum
distances achievable with other technologies are indicated for
comparison.
[0051] Figure 7 illustrates the phasing accuracy for a sample
with well-characterized haplotypes, NA12878. Indicated distances
are those between the SNPs being phased.
[0052] Figure 8 illustrates various components of an exemplary
computer system according to various embodiments of the present
disclosure.
[0053] Figure 9 is a block diagram illustrating the
architecture of an exemplary computer system that can be used in
connection with various embodiments of the present disclosure.
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[0054] Figure 10 is a diagram illustrating an exemplary
computer network that can be used in connection with various
embodiments of the present disclosure.
[0055] Figure 11 is a block diagram illustrating the
architecture of another exemplary computer system that can be used
in connection with various embodiments of the present disclosure.
DETAILED DESCRIPTION
[00561 As used herein and in the appended claims, the singular
forms "a," "and," and "the" include plural referents unless the
context clearly dictates otherwise. Thus, for example, reference
to "contig" includes a plurality of such contigs and reference to
"probing the physical layout of chromosomes" includes reference to
one or more methods for probing the physical layout of chromosomes
and equivalents thereof known to those skilled in the art, and so
forth.
[0057] Also, the use of "and" means "and/or" unless stated
otherwise. Similarly, "comprise," "comprises," "comprising"
"include," "includes," and "including" are interchangeable and not
intended to be limiting.
[0058] It is to be further understood that where descriptions
of various embodiments use the term "comprising," those skilled in
the art would understand that in some specific instances, an
embodiment can be alternatively described using language
"consisting essentially of" or "consisting of."
[0059] The term "sequencing read" as used herein, refers to a
fragment of DNA in which the sequence has been determined.
[0060] The term "contigs" as used herein, refers to contiguous
regions of DNA sequence. "Contigs" can be determined by any number
methods known in the art, such as, by comparing sequencing reads
for overlapping sequences, and/or by comparing sequencing reads
against a databases of known sequences in order to identify which
sequencing reads have a high probability of being contiguous.
[0061] The term "subject" as used herein can refer to any
eukaryotic or prokaryotic organism.
[0062] The term "naked DNA" as used herein can refer to DNA
that is substantially free of complexed proteins. For example, it
can refer to DNA complexed with less than about 50%, about 40%,
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about 30%, about 20%, about 10%, about 5%, or about 1% of the
endogenous proteins found in the cell nucleus.
[0063] The term "reconstituted chromatin" as used herein can
refer to forming chromatin formed by complexing isolated nuclear
proteins to naked DNA.
[0064] The term "read pair" or "read-pair" as used herein can
refer to two or more elements that are linked to provide sequence
information. In some cases, the number of read-pairs can refer to
the number of mappable read-pairs. In other cases, the number of
read-pairs can refer to the total number of generated read-pairs.
[0065] Unless defined otherwise, all technical and scientific
terms used herein have the same meaning as commonly understood to
one of ordinary skill in the art to which this disclosure belongs.
Although any methods and reagents similar or equivalent to those
described herein can be used in the practice of the disclosed
methods and compositions, the exemplary methods and materials are
now described.
[0066] The disclosure provides methods for generating extremely
long-range read pairs and to utilize that data for the advancement
of all of the aforementioned pursuits. In some embodiments, the
disclosure provides methods that produce a highly contiguous and
accurate human genomic assembly with only -300 million read pairs.
In other embodiments, the disclosure provides methods that phase
90% or more of heterozygous variants in a human genome with 99% or
greater accuracy. Further, the range of the read pairs generated by
the disclosure can be extended to span much larger genomic
distances. The assembly is produced from a standard shotgun library
in addition to an extremely long-range read pair library. In yet
other embodiments, the disclosure provides software that is capable
of utilizing both of these sets of sequencing data. Phased variants
are produced with a single long-range read pair library, the reads
from which are mapped to a reference genome and then used to assign
variants to one of the individual's two parental chromosomes.
Finally, the disclosure provides for the extraction of even larger
DNA fragments using known techniques, so as to generate
exceptionally long reads.
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[0067] The mechanism by which these repeats obstruct assembly
and alignment processes is fairly straightforward and is ultimately
a consequence of ambiguity (FIG. 5). In the case of large
repetitive regions the difficulty is one of span. If a read or read
pair is not long enough to span a repetitive region, one cannot
confidently connect regions bordering the repetitive element. In
the case of smaller repetitive elements the problem is primarily
placement. When a region is flanked by two repetitive elements that
are common in the genome, determining its exact placement becomes
difficult if not impossible due to the similarity of the flanking
elements to all others of their class. In both cases it is the lack
of distinguishing information in the repeat that makes the
identification, and thus placement of a particular repeat
challenging. What is needed is the ability to experimentally
establish connection between unique segments hemmed or separated by
repetitive regions.
[0068] The methods of the disclosure greatly advance the field
of genomics by overcoming the substantial barriers posed by these
repetitive regions, and can thereby enable important advances in
many domains of genomic analysis. To perform a de novo assembly
with previous technologies, one must either settle for an assembly
fragmented into many small scaffolds or commit substantial time and
resources to producing a large-insert library or using other
approaches to generate a more contiguous assembly. Such approaches
may include acquiring very deep sequencing coverage, constructing
BAC or fosmid libraries, optical mapping, or, most likely, some
combination of these and other techniques. The intense resource and
time requirements put such approaches out of reach for most small
labs and prevents studying non-model organisms. Since the methods
described herein can produce very long-range read pairs, de novo
assembly can be achieved with a single sequencing run. This would
cut assembly costs by orders of magnitude and shorten the time
required from months or years to weeks. In some cases, the methods
disclosed herein allow for generating a plurality of read-pairs in
less than 14 days, less than 13 days, less than 12 days, less than
11 days, less than 10 days, less than 9 days, less than 8 days,
less than 7 days, less than 6 days, less than 5 days, less than 4
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days, or in a range between any two of foregoing specified time
periods. For example, the methods can allow for generating a
plurality of read-pairs in about 10 days to 14 days. Building
genomes for even the most niche of organisms would become routine,
phylogenetic analyses would suffer no lack of comparisons, and
projects such as Genome 10k could be realized.
[0069] Similarly, structural and phasing analyses for medical
purposes also remain challenging. There is astounding heterogeneity
among cancers, individuals with the same type of cancer, or even
within the same tumor. Teasing out the causative from consequential
effects requires very high precision and throughput at a low per-
sample cost. In the domain of personalized medicine, one of the
gold standards of genomic care is a sequenced genome with all
variants thoroughly characterized and phased, including large and
small structural rearrangements and novel mutations. To achieve
this with previous technologies demands effort akin to that
required for a de novo assembly, which is currently too expensive
and laborious to be a routine medical procedure. The disclosed
methods can rapidly produce complete, accurate genomes at low cost
and can thereby yield many highly sought capabilities in the study
and treatment of human disease.
[0070] Finally, applying the methods disclosed herein to
phasing can combine the convenience of statistical approaches with
the accuracy of familial analysis, providing savings - money,
labor, and samples - than using either method alone. De novo
variant phasing, a highly desirable phasing analysis that is
prohibitive with previous technologies, can be performed readily
using the methods disclosed herein. This is particularly important
as the vast majority of human variation is rare (less than 5% minor
allele frequency). Phasing information is valuable for population
genetic studies that gain significant advantages from networks of
highly connected haplotypes (collections of variants assigned to a
single chromosome), relative to unlinked genotypes. Haplotype
information can enable higher resolution studies of historical
changes in population size, migrations, and exchange between
subpopulations, and allows us to trace specific variants back to
particular parents and grandparents. This in turn clarifies the
-16-
Date Recue/Date Received 2023-08-15
genetic transmission of variants associated with disease, and the
interplay between variants when brought together in a single
individual. The methods of the disclosure can eventually enable the
preparation, sequencing, and analysis of extremely long range read
pair (XLRP) libraries.
[0071] In some embodiments of the disclosure, a tissue or a DNA
sample from a subject can be provided and the method can return an
assembled genome, alignments with called variants (including large
structural variants), phased variant calls, or any additional
analyses. In other embodiments, the methods disclosed herein can
provide XLRP libraries directly for the individual.
[0072] In various embodiments of the disclosure, the methods
disclosed herein can generate extremely long-range read pairs
separated by large distances. The upper limit of this distance may
be improved by the ability to collect DNA samples of large size. In
some cases, the read pairs can span up to50, 60, 70, 80, 90, 100,
125, 150, 175, 200, 225, 250, 300, 400, 500, 600, 700, 800, 900,
1000, 1500, 2000, 2500, 3000, 4000, 5000 kbp or more in genomic
distance. In some examples, the read pairs can span up to 500 kbp
in genomic distance. In other examples, the read pairs can span up
to 2000 kbp in genomic distance. The methods disclosed herein can
integrate and build upon standard techniques in molecular biology,
and are further well-suited for increases in efficiency,
specificity, and genomic coverage. In some cases, the read pairs
can be generated in less than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 60, or 90 days. In some examples, the read pairs can be
generated in less than about 14 days. In further examples, the read
pairs can be generated in less about 10 days. In some cases, the
methods of the present disclosure can provide greater than about
53, about 10%, about 15 t, about 20%, about 30%, about 40%, about
50%, about 60%, about 70%, about 80%, about 90%, about 95%, about
99%, or about 100% of the read pairs with at least about 50%, about
60%, about 70%, about 80%, about 90%, about 95%, about 99%, or
about 100% accuracy in correctly ordering and/or orientating the
plurality of contigs. For example, the methods can provide about 90
-17-
Date Recue/Date Received 2023-08-15
to 100% accuracy in correctly ordering and/or orientating the
plurality of contigs.
[0073] In other embodiments, the methods disclosed herein can
be used with currently employed sequencing technology. For
example, the methods can be used in combination with well-tested
and/or widely deployed sequencing instruments. In further
embodiments, the methods disclosed herein can be used with
technologies and approaches derived from currently employed
sequencing technology.
[0074] The methods of the disclosure dramatically simplify de
novo genomic assembly for a wide range of organisms. Using previous
technologies, such assemblies are currently limited by the short
inserts of economical mate-pair libraries. While it may be possible
to generate read pairs at genomic distances up to the 40-50 kbp
accessible with fosmids, these are expensive, cumbersome, and too
short to span the longest repetitive stretches, including those
within centromeres, which in humans range in size from 300 kbp to 5
mbp. The methods disclosed herein can provide read pairs capable of
spanning large distances (e.g., megabases or longer) and thereby
overcome these scaffold integrity challenges. Accordingly,
producing chromosome-level assemblies can be routine by utilizing
the methods of the disclosure. More laborious avenues for assembly
- currently costing research labs incredible amounts of time and
money, and prohibiting expansive genomic catalogs - may become
unnecessary, freeing up resources for more meaningful analyses.
Similarly, the acquisition of long-range phasing information can
provide tremendous additional power to population genomic,
phylogenetic, and disease studies. The methods disclosed herein
enable accurate phasing for large numbers of individuals, thus
extending the breadth and depth of our ability to probe genomes at
the population and deep-time levels.
[0075] In the realm of personalized medicine, the XLRP read
pairs generated from the methods disclosed herein represents a
meaningful advance toward accurate, low-cost, phased, and rapidly
produced personal genomes. Current methods are insufficient in
their ability to phase variants at long distances, thereby
preventing the characterization of the phenotypic impact of
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Date Recue/Date Received 2023-08-15
compound heterozygous genotypes. Additionally, structural variants
of substantial interest for genomic diseases are difficult to
accurately identify and characterize with current techniques due to
their large size in comparison to reads and read pair inserts used
to study them. Read pairs spanning tens of kilobases to megabases
or longer can help alleviate this difficulty, thereby allowing for
highly parallel and personalized analyses of structural variation.
[0076] Basic evolutionary and biomedical research is being
driven by technological advances in high-throughput sequencing.
Whereas whole genome sequencing and assembly used to be the
provenance of large genome sequencing centers, commercially
available sequencers are now inexpensive enough that most research
universities have one or several of these machines. It is now
relatively inexpensive to generate massive quantities of DNA
sequence data. However it remains difficult in theory and in
practice to produce high-quality, highly contiguous genome
sequences with current technology. Furthermore, because most
organisms that one would care to analyze, including humans, are
diploid, each individual has two haploid copies of the genome. At
sites of heterozygosity (e.g., where the allele given by the mother
differs from the allele given by the father), it is difficult to
know which sets of alleles came from which parent (known as
haplotype phasing). This information can be used for performing a
number of evolutionary and biomedical studies such as disease and
trait association studies.
[0077] In various embodiments, the disclosure provides methods
for genome assembly that combine technologies for DNA preparation
with paired-end sequencing for high-throughput discovery of short,
intermediate and long term connections within a given genome. The
disclosure further provides methods using these connections to
assist in genome assembly, for haplotype phasing, and/or for
metagenomic studies. While the methods presented herein can be
used to determine the assembly of a subject's genome, it should
also be understood that the methods presented herein can also be
used to determine the assembly of portions of the subject's genome
such as chromosomes, or the assembly of the subject's chromatin of
varying lengths.
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Date Recue/Date Received 2023-08-15
[0078] In some embodiments, the disclosure provides for one or
more methods disclosed herein that comprise the step of generating
a plurality of contigs from sequencing fragments of target DNA
obtained from a subject. Long stretches of target DNA can be
fragmented by cutting the DNA with one or more restriction enzymes,
shearing the DNA, or a combination thereof. The resulting
fragments can be sequenced using high throughput sequencing methods
to obtain a plurality of sequencing reads. Examples of high
throughput sequencing methods which can be used with the methods of
the disclosure include, but are not limited to, 454 pyrosequencing
methods developed Roche Diagnostics, "clusters" sequencing methods
developed by Illumina, SOLiD and Ion semiconductor sequencing
methods developed by Life Technologies, and DNA nanoball sequencing
methods developed by Complete Genomics. Overlapping ends of
different sequencing reads can then be assembled to form a contig.
Alternatively, fragmented target DNA can be cloned into vectors.
Cells or organisms are then transfected with the DNA vectors to
form a library. After replicating the transfected cells or
organisms, the vectors are isolated and sequenced to generate a
plurality of sequencing reads. The overlapping ends of different
sequencing reads can then be assembled to form a contig.
[0079] As shown in FIG. 1, genome assembly, especially with
high-throughput sequencing technology can be problematic. Often,
the assembly consists of thousands or tens of thousands of short
contigs. The order and orientation of these contigs is generally
unknown, limiting the usefulness of the genome assembly.
Technologies exist to order and orient these scaffolds, but they
are generally expensive, labor intensive, and often fail in
discovering very long range interactions.
[0080] Samples comprising target DNA used to generate contigs
can be obtained from a subject by any number of means, including by
taking bodily fluids (e.g., blood, urine, serum, lymph, saliva,
anal and vaginal secretions, perspiration and semen), taking
tissue, or by collecting cells/organisms. The sample obtained may
be comprised of a single type of cell/organism, or may be comprised
multiple types of cells/organisms. The DNA can be extracted and
prepared from the subject's sample. For example, the sample may be
Date Recue/Date Received 2023-08-15
treated to lyse a cell comprising the polynucleotide, using known
lysis buffers, sonication techniques, electroporation, and the
like. The target DNA may be further purified to remove
contaminants, such as proteins, by using alcohol extractions,
cesium gradients, and/or column chromatography.
[0081] In other embodiments of the disclosure, a method to
extract very high molecular weight DNA is provided. In some cases,
the data from an XLRP library can be improved by increasing the
fragment size of the input DNA. In some examples, extracting
megabase-sized fragments of DNA from a cell can produce read pairs
separated by megabases in the genome. In some cases, the produced
read-pairs can provide sequence information over a span of greater
than about 10 kB, about 50 kB, about 100 kB, about 200 kB, about
500 kB, about 1 Mb, about 2 Mb, about 5 Mb, about 10 Mb, or about
100 Mb. In some examples, the read-pairs can provide sequence
information over a span of greater than about 500 kB. In further
examples, the read-pairs can provide sequence information over a
span of greater than about 2 Mb. In some cases, the very high
molecular weight DNA can be extracted by very gentle cell lysis
(Teague, B. et al. (2010) Proc. Nat. Acad. Sci. USA 107(24), 10848-
53) and agarose plugs (Schwartz, D. C., & Cantor, C. R. (1984)
Cell, 37(1), 67-75). In other cases, commercially available
machines that can purify DNA molecules up to megabases in length
can be used to extract very high molecular weight DNA.
[0082] In various embodiments, the disclosure provides for one
or more methods disclosed herein that comprise the step of probing
the physical layout of chromosomes within living cells. Examples
of techniques to probe the physical layout of chromosomes through
sequencing include the "C" family of techniques, such as chromosome
conformation capture ("3C"), circularized chromosome conformation
capture ("4C"), carbon-copy chromosome capture ("5C"), and Hi-C
based methods; and ChIP based methods, such as ChIP-loop, ChIP-PET.
These techniques utilize the fixation of chromatin in live cells to
cement spatial relationships in the nucleus. Subsequent processing
and sequencing of the products allows a researcher to recover a
matrix of proximate associations among genomic regions. With
further analysis these associations can be used to produce a three-
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Date Recue/Date Received 2023-08-15
dimensional geometric map of the chromosomes as they are physically
arranged in live nuclei. Such techniques describe the discrete
spatial organization of chromosomes in live cells, and provide an
accurate view of the functional interactions among chromosomal
loci. One issue that plagued these functional studies was the
presence of nonspecific interactions, associations present in the
data that are attributable to nothing more than chromosomal
proximity. In the disclosure, these nonspecific intrachromosomal
interactions are captured by the methods presented herein so as to
provide valuable information for assembly.
[0083] In some embodiments, the intrachromosomal interactions
correlate with chromosomal connectivity. In some cases, the
intrachromosomal data can aid genomic assembly. In some cases, the
chromatin is reconstructed in vitro. This can be advantageous
because chromatin - particularly histones, the major protein
component of chromatin - is important for fixation under the most
common -"c" family of techniques for detecting chromatin
conformation and structure through sequencing: 3C, 4C, SC, and Hi-
C. Chromatin is highly non-specific in terms of sequence and will
generally assemble uniformly across the genome. In some cases, the
genomes of species that do not use chromatin can be assembled on a
reconstructed chromatin and thereby extend the horizon for the
disclosure to all domains of life.
[0084] A chromatin conformation capture technique is summarized
in FIG. 2. In brief, cross-links are created between genome regions
that are in close physical proximity. Crosslinking of proteins
(such as histones) to the DNA molecule, e.g. genomic DNA, within
chromatin can be accomplished according to a suitable method
described in further detail elsewhere herein or otherwise known in
the art. In some cases, two or more nucleotide sequences can be
cross-linked via proteins bound to one or more nucleotide
sequences. One approach is to expose the chromatin to ultraviolet
irradiation (Gilmour et al., Proc. Nat'l. Acad. Sci. USA 81:4275-
4279, 1984). Crosslinking of polynucleotide segments may also be
performed utilizing other approaches, such as chemical or physical
(e.g. optical) crosslinking. Suitable chemical crosslinking agents
include, but are not limited to, formaldehyde and psotalen (Solomon
-22-
Date Recue/Date Received 2023-08-15
et al., Proc. NatL. Acad. Sci. USA 82:6470-6474, 1985; Solomon et
al., Cell 53:937-947, 1988). For example, cross-linking can be
performed by adding 296 formaldehyde to a mixture comprising the DNA
molecule and chromatin proteins. Other examples of agents that can
be used to cross-link DNA include, but are not limited to, UV
light, mitomycin C, nitrogen mustard, melphalan, 1,3-butadiene
diepoxide, cis diaminedichloroplatinum(II) and cyclophosphamide.
Suitably, the cross-linking agent will form cross-links that bridge
relatively short distances-such as about 2 A-thereby selecting
intimate interactions that can be reversed.
[0085] In some embodiments, the DNA molecule may be
immunoprecipitated prior to or after crosslinking. In some cases,
the DNA molecule can be fragmented. Fragments may be contacted with
a binding partner, such as an antibody that specifically recognizes
and binds to acetylated histones, e.g., R3. Examples of such
antibodies include, but are not limited to, Anti Acetylated Histone
R3, available from Upstate Biotechnology, Lake Placid, N.Y. The
polynucleotides from the immunoprecipitate can subsequently be
collected from the immunoprecipitate. Prior to fragmenting the
chromatin, the acetylated histones can be crosslinked to adjacent
polynucleotide sequences. The mixture is then treated to
fractionate polynucleotides in the mixture. Fractionation
techniques are known in the art and include, for example, shearing
techniques to generate smaller genomic fragments. Fragmentation can
be accomplished using established methods for fragmenting
chromatin, including, for example, sonication, shearing and/or the
use of restriction enzymes. The restriction enzyme can have a
restriction site of 1, 2, 3, 4, 5, or 6 bases long. Examples of
restriction enzymes include but are not limited to AatII, Acc65I,
Accl, AciI, AclI, AcuI, AfeI, AflII, AflIII, AgeI, Ahdl, Alel,
AluI, Alwi, AlwNI, Ape', ApaLI, ApeKI, ApoI, AscI, Asel, AsiSI,
AvaI, Avail, AvrII, BaeGI, Baer, Bernal, Ban!, BanII, BbsI, BbvCI,
BbvI, BccI, BceAI, BcgI, BciVI, Boll, Beal, BfuAI, BfuCI, BglI,
BglII, BlpI, BmgBI, BmrI, BmtI, BpmI, 8pu10I1 BpuEI, Bsara, BsaBI,
BsaHI, Baal, BsaJI, BsaWI, BsaXI, BscRI, BscYI, BegI, BsiEI,
BsiHKAI, BsiNI, Bs1I, BsmAI, BsmBI, BsmFI, Bsml, BsoBI, Bsp12861,
BspCNI, BspDI, BspEI, BspHI, BspMI, Bsp(21, Bsr8i, BsiD1, BsrFI,
-1121-
Date Recue/Date Received 2023-08-15
BsrGI, Bari, BssHII, BssKI, BssSI, BstAPI, BstBI, BstElI, BstNI,
BstUI, BstXI, BstYI, BstZ17I, Bsu36I, BtgI, BtgZI, BtsCI, BtsI,
Cac8I, ClaI, CspCI, CviAII, CviKI-1, CviQl, DdcI, Dpnl, ppnII,
DraI, Drain, DrdI, EacI, EagI, Earl, EciI, Eco53k1, EcoNI,
Eco0109I, EcoP15I, EcoRI, EcoRV, FatI, Paul, Fnu4HI, FokI, FseI,
FspI, HaeII, HaeIII, HgaI, HhaI, HincII, HindIII, HinfI, HinP11,
RpaI, HpaII, RphI, Rpy16611, Rpy1881, Rpy188III, Rpy991, RpyAV,
RpyCR4rV, RpyCR4V, Rae, RpnI, MboI, MboII, MfeI, MluI,
MlyIõ MmeI, I4n1I, MscI, MseI, Ms1I, MspAlI, MspI, MwoI, NaeI,
Nb.BbvCI, Nb.BsmI, Nb.BsrDli Nb.Btst, NciI, Neal, Ndel, NgoMIV,
NlaIII, NiaIV, NmeAIII, NotI, NruI, Nail, NspI, Nt.Alwl,
Nt.BbvCI, Nt.BsmAI, Nt.BspQI, Nt.BstNBI, Nt.CviPII, Pad, PaeR7I,
PciI, Pf1FI, 1?f1MI, PhoI, PleI, Pmei, Pm1I, ppuMI, PshAI, Pail,
PspGI, PepOMI, PspXI, PstI, PvuI, PvuII, Real, RsrII, Sad, SacII,
Sall, SapI, Sau3AI, Sau96I, SbfI, Scat, ScrFI, SexAI, SfaNI, SfcI,
SfiI, SfoI, SgrAI, SmaI, Sm1I, SnaBI, SpeI, SphI, SspI, StuI,
StyD4I, StyI, Swai, T, TagoI, TiI, Tlii, TseI, Tsp45I, Tsp5091,
TspMI, TspRI, Tth111I, Xbar, XcmI, XhoI, XmaI, XMnI, and ZraI. The
resulting fragments can vary in size. The resulting fragments may
also comprise a single-stranded overhand at the 5' or 3' end.
[0086] In some embodiments, using sonication techniques,
fragments of about 100 to 5000 nucleotides can be obtained.
Alternatively, fragments of about 100 to 1000, about 150 to 1000,
about 150 to 500, about 200 to 500, or about 200 to 400 nucleotides
can be obtained. The sample can be prepared for sequencing of
coupled sequence segments that are cross-linked. In some cases, a
single, short stretch of polynucleotide can be created, for
example, by ligating two sequence segments that were
intramolecularly crosslinked. Sequence information may be obtained
from the sample using any suitable sequencing technique described
in further detail elsewhere herein or otherwise known in the art,
such as a high throughput sequencing method. For example, ligation
products can be subjected to paired-end sequencing obtaining
sequence information from each end of a fragment. Pairs of sequence
segments can be represented in the obtained sequence information,
associating haplotyping information over a linear distance
separating the two sequence segments along the polynucleotide.
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Date Recue/Date Received 2023-08-15
[0087] One feature of the data generated by Hi-C is that most
reads pairs, when mapped back to the genome, are found to be in
close linear proximity. That is, most read pairs are found to be
close to one another in the genome. In the resulting data sets, the
probability of intrachromosomal contacts is on average much higher
than that of interchromosomal contacts, as expected if chromosomes
occupy distinct territories. Moreover, although the probability of
interaction decays rapidly with linear distance, even loci
separated by > 200 Mb on the same chromosome are more likely to
interact than loci on different chromosomes. In detecting long-
range intra-chromosomal and especially inter-chromosomal contacts,
this "background" of short and intermediate range intra-chromosomal
contacts are background noise to be factored out using Hi-C
analysis.
[0088] Notably, Hi-C experiments in eukaryotes have shown, in
addition to species-specific and cell type-specific chromatin
interactions, two canonical interaction patterns. One pattern,
distance-dependent decay (DDD), is a general trend of decay in
interaction frequency as a function of genomic distance. The second
pattern, cis-trans ratio (CTR), is a significantly higher
interaction frequency between loci located on the same chromosome,
even when separated by tens of megabases of sequence, versus loci
on different chromosomes. These patterns may reflect general
polymer dynamics, where croximal loci have a higher probability of
randomly interacting, as well as specific nuclear organization
features such as the formation of chromosome territories, the
phenomenon of interphase chromosomes tending to occupy distinct
volumes in the nucleus with little mixing. Although the exact
details of these two patterns may vary between species, cell types
and cellular conditions, they are ubiquitous and prominent. These
patterns are so strong and consistent that they are used to assess
experiment quality and are usually normalized out of the data in
order to reveal detailed interactions. However, in the methods
disclosed herein, genome assembly can take advantage of the three-
dimensional structure of genomes. Features which make the canonical
Hi-C interaction patterns a hindrance for the analysis of specific
looping interactions, namely their ubiquity, strength and
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DateRecue/DateReceived2023-08-15
consistency, can be used as powerful tool for estimating the
genomic position of contigs.
[0069] In a particular implementation, examination of the
physical distance between intra-chromosomal read pairs indicates
several useful features of the data with respect to genome
assembly. First, shorter range interactions are more common than
longer-range interactions (e.g., see FIG. 6). That is, each read of
a read-pair is more likely to be mated with a region close by in
the actual genome than it is to be with a region that is far away.
Second, there is a long tail of intermediate and long-range
interactions. That is, read-pairs carry information about intra-
chromosomal arrangement at kilobase (kB) or even megabase (Mb)
distances. For example, read-pairs can provide sequence information
over a span of greater than about 10 kB, about 50 kB, about 100 kB,
about 200 kB, about 500 kB, about 1 Mb, about 2 Mb, about 5 Mb,
about 10 Mb, or about 100 Mb. These features of the data simply
indicate that regions of the genome that are nearby on the same
chromosome are more likely to be in close physical proximity - an
expected result because they are chemically linked to one another
through the DNA backbone. It was speculated that genome-wide
chromatin interaction data sets, such as those generated by Hi-C.,
would provide long-range information about the grouping and linear
organization of sequences along entire chromosomes.
[0090] Although the experimental methods for Hi-C are
straightforward and relatively low cost, current protocols for
genome assembly and haplotyping require 106-108 cells, a fairly
large amount of material that may not be feasible to obtain,
particularly from certain human patient samples. By contrast, the
methods disclosed herein include methods that allow for accurate
and predictive results for genotype assembly, haplotype phasing,
and metagenomics with significantly less material from cells. For
example, less than about 0.1 pig, about 0.2 pig, about 0.3 pig, about
0.4 jig, about 0.5 pig, about 0.6 pig, about 0.7 pig, about 0.8 pig,
about 0.9 gg, about 1.0 pig, about 1.2 pig, about 1.4 pig, about 1.6
gg, about 1.8 pig, about 2.0 pig, about 2.5 pig, about 3.0 pig, about
3.5 pig, about 4.0 pig, about 4.5 pig, about 5.0 pig, about 6.0 pig,
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Date Recue/Date Received 2023-08-15
about 7.0 pg, about 8.0 pg, about 9.0 pg, about 10 pg, about 15 pg,
about 20 pg, about 30 pg. about 40 pg, about 50 pg, about 60 pg,
about 70 pg. about 80 pg. about 90 pg, about 100pg, about 150 pg,
about 200 pg, about 300 pg, about 400 pg, about 500 pg, about 600
pg, about 700 pg, about 800 pg, about 900 pg, or about 1000 pg of
DNA can be used with the methods disclosed herein. In some
examples, the DNA used in the methods disclosed herein can be
extracted from less than about 1,000,000, about 500,000, about
100,000, about 50,000, about 10,000, about 5,000, about 1,000,
about 5,000, or about 1,000, about 500, or about 100 cells.
[0091] Universally, procedures for probing the physical layout
of chromosomes, such as Hi-C based techniques, utilize chromatin
that is formed within a cell/organism, such as chromatin isolated
from cultured cells or primary tissue. The disclosure provides not
only for the use of such techniques with chromatin isolated from a
cell/organism but also with reconstituted chromatin. Reconstituted
chromatin is differentiated from chromatin formed within a
cell/organism over various features. First, for many samples, the
collection of naked DNA samples can be achieved by using a variety
of noninvasive to invasive methods, such as by collecting bodily
fluids, swabbing buccal or rectal areas, taking epithelial samples,
etc. Second, reconstituting chromatin substantially prevents the
formation of inter-chromosomal and other long-range interactions
that generate artifacts for genome assembly and haplotype phasing.
In some cases, a sample may have less than about 20, 15, 12, 11,
10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0.5, 0.4, 0.3, 0.2, 0.1% or less
inter-chromosomal or intermolecular crosslinking according to the
methods and compositions of the disclosure. In some examples, the
sample may have less than about 5t inter-chromosomal or
intermolecular crosslinking. In some examples, the sample may have
less than about 3% inter-chromosomal or intermolecular
crosslinking. In further examples, may have less than about 1%
inter-chromosomal or intermolecular crosslinking. Third, the
frequency of sites that are capable of crosslinking and thus the
frequency of intramolecular crosslinks within the polynucleotide
can be adjusted. For example, the ratio of DNA to histones can be
varied, such that the nucleosome density can be adjusted to a
Date Recue/Date Received 2023-08-15
desired value. In some cases, the nucleosome density is reduced
below the physiological level. Accordingly, the distribution of
crosslinks can be altered to favor longer-range interactions. /n
some embodiments, sub-samples with varying cross-linking density
may be prepared to cover both short- and long-range associations.
For example, the crosslinking conditions can be adjusted such that
at least about 1%, about 2%, about 3%, about 4%, about 5%, about
6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%,
about 13%, about 14%, about 15%, about 16%, about 17%, About 18%,
about 19%, about 20%, about 25%, about 30%, about 40%, about 45%,
about 50%, about 60%, About 70%, about 80%, about 90%, About 95%,
or about 100% of the crosslinks occur between DNA segments that are
at least about 50 kb, About 60 kb, about 70 kb, about 80 kb, about
90 kb, about 100 kb, about 110 kb, about 120 kb, about 130 kb,
about 140 kb, about 150 kb, about 160 kb, about 180 kb, about 200
kb, about 250 kb, About 300 kb, about 350 kb, about 400 kb, about
450 kb, or about 500 kb apart on the sample DNA molecule.
[0092] In various embodiments, the disclosure provides a
variety of methods that enable the mapping of the plurality of read
pairs to the plurality of contigs. There are several publicly
available computer programs for mapping reads to contig sequences.
These read-mapping programs data also provide data describing how
unique a particular read-mapping is within the genome. From the
population of reads that map uniquely, with high confidence within
a contig, we can infer the distribution of distances between reads
in each read pair. These are the data shown in FIG. 6. For read
pairs whose reads map confidently to different contigs, this
mapping data implies a connection between the two contigs in
question. It also implies a distance between the two contigs that
is proportional to the distribution of distances learned from the
analysis described above. Thus, each read pair whose reads map to
different contigs implies a connection between those two contigs in
a correct assembly. The connections inferred from all such mapped
read pairs can be summarized in an adjacency matrix wherein each
contig is represented by both a row and column. Read pairs that
connect contigs are marked as a non-zero value in the corresponding
row and column denoting the contigs to which the reads in the read
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Date Recue/Date Received 2023-08-15
pair were mapped. Most of the read pairs will map within in a
contig, and from which the distribution of distances between read
pairs can be learned, and from which an adjacency matrix of contigs
can be constructed using read pairs that map to different contigs.
[0093] In various embodiments, the disclosure provides methods
comprising constructing an adjacency matrix of contigs using the
read-mapping data from the read-pair data. In some embodiments,
the adjacency matrix uses a weighting scheme for read pairs that
incorporate the tendency for short-range interactions over long-
range interactions (e.g., see FIG. 3). Read pairs spanning shorter
distances are generally more common than read pairs that span
longer distances. A function describing the probability of a
particular distance can be fit using the read pair data that map to
a single contig to learn this distribution. Therefore, one
important feature of read pairs that map to different contigs is
the position on the contig where they map. For read pairs that both
map near one end of a contig, the inferred distance between these
contigs can be short and therefore the distance between the joined
reads small. Since shorter distances between read pairs are more
common than longer distances, this configuration provides stronger
evidence that these two contigs are adjacent than would reads
mapping far from the edges of the contig. Therefore, the
connections in the adjacency matrix are further weighted by the
distance of the reads to the edge of the contigs. In further
embodiments, the adjacency matrix can further be re-scaled to down-
weight the high number of contacts on some contigs that represent
promiscuous regions of the genome. These regions of the genome,
identifiable by having a high proportion of reads mapping to them,
are a priori more likely to contain spurious read mappings that
might misinform assembly. In yet further embodiments, this scaling
can be directed by searching for one or more conserved binding
sites for one or more agents that regulate the scaffolding
interactions of chromatin, such as transcriptional repressor CTCF,
endocrine receptors, cohesins, or covalently modified histones.
[0094] In some embodiments, the disclosure provides for one or
more methods disclosed herein that comprise a step of analyzing the
adjacency matrix to determine a path through the contigs that
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represent their order and/or orientation to the genome. In other
embodiments, the path through the contigs can be chosen so that
each contig is visited exactly once. In further embodiments, the
path through the contigs is chosen so that the path through the
adjacency matrix maximizes the sum of edge-weights visited. In this
way, the most probably contig connections are proposed for the
correct assembly. In yet further embodiments, the path through the
contigs can be chosen so that each contig is visited exactly once
and that edge-weighting of adjacency matrix is maximized.
[0095] In diploid genomes, it often important to know which
allelic variants are linked on the same chromosome. This is known
as the haplotype phasing. Short reads from high-throughput sequence
data rarely allow one to directly observe which allelic variants
are linked. Computational inference of haplotype phasing can be
unreliable at long distances. The disclosure provides one or
methods that allow for determining which allelic variants are
linked using allelic variants on read pairs.
[0096] In various embodiments, the methods and compositions of
the disclosure enable the haplotype phasing of diploid or polyploid
genomes with regard to a plurality of allelic variants. The
methods described herein can thus provide for the determination of
linked allelic variants are linked based on variant information
from read pairs and/or assembled contigs using the same. Examples
of allelic variants include, but are not limited to those that are
known from the 1000genomes, UK1OK, HapMap and other projects for
discovering genetic variation among humans. Disease association to
a specific gene can be revealed more easily by having haplotype
phasing data as demonstrated, for example, by the finding of
unlinked, inactivating mutations in both copies SH3TC2 leading to
Charcot-Marie-Tooth neuropathy (Lupski JR, Reid JG, Gonzaga-
Jauregui C, et al. N. Engl. J. Med. 362:1181-91, 2010) and
unlinked, inactivating mutations in both copies of ABCG5 leading to
hypercholesterolemia 9 (Rios J, Stein E, Shendure J, et al. Hum.
Mol. Genet. 19:4313-18, 2010).
[0097] Humans are heterozygous at an average of 1 site in
1,000. In some cases, a single lane of data using high throughput
sequencing methods can generate at least about 150,000,000 read
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pairs. Read pairs can be about 100 base pairs long. From these
parameters, one-tenth of all reads from a human sample is estimated
to cover a heterozygous site. Thus, on average one-hundredth of all
read pairs from a human sample is estimated to cover a pair of
heterozygous sites. Accordingly, about 1,500,000 read pairs (one-
hundredth of 150,000,000) provide phasing data using a single lane.
With approximately 3 billion bases in the human genome, and one in
one-thousand being heterozygous, there are approximately 3 million
heterozygous sites in an average human genome. With about 1,500,000
read pairs that represent a pair of heterozygous sites, the average
coverage of each heterozygous site to be phased using a single lane
of a high throughput sequence method is about (lx), using a typical
high throughput sequencing machine. A diploid human genome can
therefore be reliably and completely phased with one lane of a
high-throughput sequence data relating sequence variants from a
sample that is prepared using the methods disclosed herein. In some
examples, a lane of data can be a set of DNA sequence read data. In
further examples, a lane of data can be a set of DNA sequence read
data from a single run of a high throughput sequencing instrument.
[0098] As the human genome consists of two homologous sets of
chromosomes, understanding the true genetic makeup of an individual
requires delineation of the maternal and paternal copies or
haplotypes of the genetic material. Obtaining a haplotype in an
individual is useful in several ways. First, haplotypes are useful
clinically in predicting outcomes for donor-host matching in organ
transplantation and are increasingly used as a means to detect
disease associations. Second, in genes that show compound
heterozygosity, haplotypes provide information as to whether two
deleterious variants are located on the same allele, greatly
affecting the prediction of whether inheritance of these variants
is harmful. Third, haplotypes from groups of individuals have
provided information on population structure and the evolutionary
history of the human race. Lastly, recently described widespread
allelic imbalances in gene expression suggest that genetic or
epigenetic differences between alleles may contribute to
quantitative differences in expression. An understanding of
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haplotype structure will delineate the mechanisms of variants that
contribute to allelic imbalances.
[0099] In certain embodiments, the methods disclosed herein
comprise an in vitro technique to fix and capture associations
among distant regions of a genome as needed for long-range linkage
and phasing. In some cases, the method comprises constructing and
sequencing an XLRP library to deliver very genomically distant read
pairs. In some cases, the interactions primarily arise from the
random associations within a single DNA fragment. In some examples,
the genomic distance between segments can be inferred because
segments that are near to each other in a DNA molecule interact
more often and with higher probability, while interactions between
distant portions of the molecule will be less frequent.
Consequently there is a systematic relationship between the number
of pairs connecting two loci and their proximity on the input DNA.
The disclosure can produce read pairs capable of spanning the
largest DNA fragments in an extraction, as demonstrated in FIG. 2.
The input DNA for this library had a maximum length of 150 kbp,
which is the longest meaningful read pair we observe from the
sequencing data. This suggests that the present method can link
still more genomically distant loci if provided larger input DNA
fragments. By applying improved assembly software tools that are
specifically adapted to handle the type of data produced by the
present method, a complete genomic assembly may be possible.
[00100] Extremely high phasing accuracy can be achieved by the
data produced using the methods and compositions of the disclosure.
In comparison to previous methods, the methods described herein can
phase a higher proportion of the variants. Phasing can be achieved
while maintaining high levels of accuracy. This phase information
can be extended to longer ranges, for example greater than about
200 kbp, about 300 kbp, about 400 kbp, about 500 kbp, about 600
kbp, about 700 kbp, about 800 kbp, about 900 kbp, about 1Mbp, about
2Mbp, about 3 Mbp, about 4 Mbp, about 5Mbp, or about 10 Mbp. In
some embodiments, more than 90% of the heterozygous SNPs for a
human sample can be phased at an accuracy greater than 99% using
less than about 250 million reads or read pairs, e.g. by using only
1 lane of Illumina HiSeq data. In other cases, more than about 40%,
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50%, 60%, 70%, 80%, 90 %, 95% or 99% of the heterozygous SNPs for a
human sample can be phased at an accuracy greater than about 70%,
80%, 90%, 95%, or 99% using less than about 250 million or about
500 million reads or read pairs, e.g. by using only 1 or 2 lanes of
Illumine HiSeq data. For example, more than 95% or 99% of the
heterozygous SNPs for a human sample can be phase at an accuracy
greater than about 95% or 99% using less about 250 million or about
500 million reads. In further cases, additional variants can be
captured by increasing the read length to about 200 bp, 250 bp, 300
bp, 350 bp, 400 bp, 450 bp, 500 bp, 600 bp, 800 bp, 1000 bp, 1500
bp, 2 kbp, 3 kbp, 4 kbp, 5 kbp, 10 kbp, 20 kbp, 50 kbp, or 100 kbp.
[00101] In other embodiments of the disclosure, the data from an
XLRP library can be used to confirm the phasing capabilities of the
long-range read pairs. As shown in FIG. 6, the accuracy of those
results is on par with the best technologies previously available,
but further extending to significantly longer distances. The
current sample preparation protocol for a particular sequencing
method recognizes variants located within a read-length, e.g. 150
bp, of a targeted restriction site for phasing. In one example,
from an XLRP library built for NA12878, a benchmark sample for
assembly, 44% of the 1,703,909 heterozygous SNPs present were
phased with an accuracy greater than 99%. In some cases, this
proportion can be expanded to nearly all variable sites with the
judicious choice of restriction enzyme or with combinations of
different enzymes.
[00102] In some embodiments, the compositions and methods
described herein allow for the investigation of meta-genomes, for
example those found in the human gut. Accordingly, the partial or
whole genomic sequences of some or all organisms that inhabit a
given ecological environment can be investigated. Examples include
random sequencing of all gut microbes, the microbes found on
certain areas of skin, and the microbes that live in toxic waste
sites. The composition of the microbe population in these
environments can be determined using the compositions and methods
described herein and as well as the aspects of interrelated
biochemistries encoded by their respective genomes. The methods
described herein can enable metagenomic studies from complex
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Date Recue/Date Received 2023-08-15
biological environments, for example, those that comprise more than
2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 20, 25, 30, 40, 50 , 60, 70,
80, 90, 100, 125, 150, 175, 200, 250, 300, 400, 500, 600, 700, 800,
900, 1000, 5000, 10000 or more organisms and/or variants of
organisms.
[00103] High degrees of accuracy required by cancer genome
sequencing can be achieved using the methods and systems described
herein. Inaccurate reference genomes can make base-calling
challenges when sequencing cancer genomes. Heterogeneous samples
and small starting materials, for example a sample obtained by
biopsy introduce additional challenges. Further, detection of large
scale structural variants and/or losses of heterozygosity is often
crucial for cancer genome sequencing, as well as the ability to
differentiate between somatic variants and errors in base-calling.
[00104] Systems and methods described herein may generate
accurate long sequences from complex samples containing 2, 3, 4, 5,
6, 7, 8, 9, 10, 12, 15, 20 or more varying genomes. Mixed samples
of normal, benign, and/or tumor origin may be analyzed, optionally
without the need for a normal control. In some embodiments,
starting samples as little as 10Ong or even as little as hundreds
of genome equivalents are utilized to generate accurate long
sequences. Systems and methods described herein may allow for
detection of large scale structural variants and rearrangements,
Phased variant calls may be obtained over long sequences spanning
about 1 kbp, about 2 kbp, about 5 kbp, about 10 kbp, 20 kbp, about
50 kbp, about 100 kbp, about 200 kbp, about 500 kbp, about 1 Mbp,
about 2 Mbp, about 5 Mbp, about 10 Mbp, about 20 Mbp, about 50 Mbp,
or about 100 Mbp or more nucleotides. For example, phase variant
call may be obtained over long sequences spanning about 1 Mbp or
about 2 Mbp.
[00105] Haplotypes determined using the methods and systems
described herein may be assigned to computational resources, for
example computational resources over a network, such as a cloud
system. Short variant calls can be corrected, if necessary, using
relevant information that is stored in the computational resources.
Structural variants can be detected based on the combined
information from short variant calls and the information stored in
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Date Recue/Date Received 2023-08-15
the computational resources. Problematic parts of the genome, such
as segmental duplications, regions prone to structural variation,
the highly variable and medically relevant MHC region, centromeric
and telomeric regions, and other heterochromatic regions including
but limited to those with repeat regions, low sequence accuracy,
high variant rates, ALE) repeats, segmental duplications, or any
other relevant problematic parts known in the art, can be
reassembled for increased accuracy.
[00106] A sample type can be assigned to the sequence
information either locally or in a networked computational
resource, such as a cloud. In cases where the source of the
information is known, for example when the source of the
information is from a cancer or normal tissue, the source can be
assigned to the sample as part of a sample type. Other sample type
examples generally include, but are not limited to, tissue type,
sample collection method, presence of infection, type of infection,
processing method, size of the sample, etc. In cases where a
complete or partial comparison genome sequence is available, such
as a normal genome in comparison to a cancer genome, the
differences between the sample data and the comparison genome
sequence can be determined and optionally output.
[00107] The methods of the can be used in the analysis of
genetic information of selective genomic regions of interest as
well as genomic regions which may interact with the selective
region of interest. Amplification methods as disclosed herein can
be used in the devices, kits, and methods known to the art for
genetic analysis, such as, but not limited to those found in U.S.
Pat. Nos. 6,449,562, 6,287,766, 7,361,468, 7,414,117, 6,225,109,
and 6,110,709. In some cases, amplification methods of the present
disclosure can be used to amplify target nucleic acid for DNA
hybridization studies to determine the presence or absence of
polymorphisms. The polymorphisms, or alleles, can be associated
with diseases or conditions such as genetic disease. In other cases
the polymorphisms can be associated with susceptibility to diseases
or conditions, for example, polymorphisms associated with
addiction, degenerative and age related conditions, cancer, and the
like. In other cases, the polymorphisms can be associated with
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Date Recue/Date Received 2023-08-15
beneficial traits such as increased coronary health, or resistance
to diseases such as HIV or malaria, or resistance to degenerative
diseases such as osteoporosis, Alzheimer's or dementia.
[00108] The compositions and methods of the disclosure can be
used for diagnostic, prognostic, therapeutic, patient
stratification, drug development, treatment selection, and
screening purposes. The present disclosure provides the advantage
that many different target molecules can be analyzed at one time
from a single biomolecular sample using the methods of the
disclosure. This allows, for example, for several diagnostic tests
to be performed on one sample.
[00109] The composition and methods of the disclosure can be
used in genomics. The methods described herein can provide an
answer rapidly which is very desirable for this application. The
methods and composition described herein can be used in the process
of finding biomarkers that may be used for diagnostics or
prognostics and as indicators of health and disease. The methods
and composition described herein can be used to screen for drugs,
e.g., drug development, selection of treatment, determination of
treatment efficacy and/or identify targets for pharmaceutical
development. The ability to test gene expression on screening
assays involving drugs is very important because proteins are the
final gene product in the body. In some embodiments, the methods
and compositions described herein will measure both protein and
gene expression simultaneously which will provide the most
information regarding the particular screening being performed.
[00110] The composition and methods of the disclosure can be
used in gene expression analysis. The methods described herein
discriminate between nucleotide sequences. The difference between
the target nucleotide sequences can be, for example, a single
nucleic acid base difference, a nucleic acid deletion, a nucleic
acid insertion, or rearrangement. Such sequence differences
involving more than one base can also be detected. The process of
the present disclosure is able to detect infectious diseases,
genetic diseases, and cancer. It is also useful in environmental
monitoring, forensics, and food science. Examples of genetic
analyses that can be performed on nucleic acids include e.g., SNP
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Date Recue/Date Received 2023-08-15
detection, STR detection, RNA expression analysis, promoter
methylation, gene expression, virus detection, viral subtyping and
drug resistance.
[00111] The present methods can be applied to the analysis of
biomolecular samples obtained or derived from a patient so as to
determine whether a diseased cell type is present in the sample,
the stage of the disease, the prognosis for the patient, the
ability to the patient to respond to a particular treatment, or the
best treatment for the patient. The present methods can also be
applied to identify biomarkers for a particular disease.
[00112] In some embodiments, the methods described herein are
used in the diagnosis of a condition. As used herein the term
"diagnose" or "diagnosis" of a condition may include predicting or
diagnosing the condition, determining predisposition to the
condition, monitoring treatment of the condition, diagnosing a
therapeutic response of the disease, or prognosis of the condition,
condition progression, or response to particular treatment of the
condition. For example, a blood sample can be assayed according to
any of the methods described herein to determine the presence
and/or quantity of markers of a disease or malignant cell type in
the sample, thereby diagnosing or staging the a disease or a
cancer.
[00113] In some embodiments, the methods and composition
described herein are used for the diagnosis and prognosis of a
condition.
[00114] Numerous immunologic, proliferative and malignant
diseases and disorders are especially amenable to the methods
described herein. Immunologic diseases and disorders include
allergic diseases and disorders, disorders of immune function, and
autoimmune diseases and conditions. Allergic diseases and
disorders include but are not limited to allergic rhinitis,
allergic conjunctivitis, allergic asthma, atopic eczema, atopic
dermatitis, and food allergy. Immunodeficiencies include but are
not limited to severe combined immunodeficiency (SCID),
hypereosinophilic syndrome, chronic granulomatous disease,
leukocyte adhesion deficiency I and II, hyper IgE syndrome, Chediak
Higashi, neutrophilias, neutropenias, aplasias, Agammaglobulinemia,
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Date Recue/Date Received 2023-08-15
hyper-IgM syndromes, DiGeorge/Velocardial-facial syndromes and
Interferon gamma-TH1 pathway defects. Autoimmune and immune
dysregulation disorders include but are not limited to rheumatoid
arthritis, diabetes, systemic lupus erythematosus, Graves' disease,
Graves ophthalmopathy, Crohn's disease, multiple sclerosis,
psoriasis, systemic sclerosis, goiter and struma lymphomatosa
(Hashimoto's thyroiditis, lymphadenoid goiter), alopecia aerata,
autoimmune myocarditis, lichen sclerosis, autoimmune uveitis,
Addison's disease, atrophic gastritis, myasthenia gravis,
idiopathic thrombocytopenic purpura, hemolytic anemia, primary
biliary cirrhosis, Wegener's granulomatosis, polyarteritis nodosa,
and inflammatory bowel disease, allograft rejection and tissue
destructive from allergic reactions to infectious microorganisms or
to environmental antigens.
[00115] Proliferative diseases and disorders that may be
evaluated by the methods of the disclosure include, but are not
limited to, hemangiomatosis in newborns; secondary progressive
multiple sclerosis; chronic progressive myelodegenerative disease;
neurofibromatosis; ganglioneuromatosis; keloid formation; Paget's
Disease of the bone; fibrocystic disease (e.g., of the breast or
uterus); sarcoidosis; Peronies and Duputren's fibrosis, cirrhosis,
atherosclerosis and vascular restenosis.
[00116] Malignant diseases and disorders that may be evaluated
by the methods of the disclosure include both hematologic
malignancies and solid tumors.
[00117] Hematologic malignancies are especially amenable to the
methods of the disclosure when the sample is a blood sample,
because such malignancies involve changes in blood-borne cells.
Such malignancies include non-Hodgkin's lymphoma, Hodgkin's
lymphoma, non-B cell lymphomas, and other lymphomas, acute or
chronic leukemias, polycythemias, thrombocythemias, multiple
myeloma, myelodysplastic disorders, myeloproliferative disorders,
myelofibroses, atypical immune lymphoproliferations and plasma cell
disorders.
[00118] Plasma cell disorders that may be evaluated by the
methods of the disclosure include multiple myeloma, amyloidosis and
Waldenstrom's macroglobulinemia.
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Date Recue/Date Received 2023-08-15
[00119] Example of solid tumors include, but are not limited to,
colon cancer, breast cancer, lung cancer, prostate cancer, brain
tumors, central nervous system tumors, bladder tumors, melanomas,
liver cancer, osteosarcoma and other bone cancers, testicular and
ovarian carcinomas, head and neck tumors, and cervical neoplasms.
[00120] Genetic diseases can also be detected by the process of
the present disclosure. This can be carried out by prenatal or
post-natal screening for chromosomal and genetic aberrations or for
genetic diseases. Examples of detectable genetic diseases include:
21 hydroxylase deficiency, cystic fibrosis, Fragile X Syndrome,
Turner Syndrome, Duchenne Muscular Dystrophy, Down Syndrome or
other trisomies, heart disease, single gene diseases, HLA typing,
phenylketonuria, sickle cell anemia, Tay-Sachs Disease,
thalassemia, Klinefelter Syndrome, Huntington Disease, autoimmune
diseases, lipidosis, obesity defects, hemophilia, inborn errors of
metabolism, and diabetes.
[00121] The methods described herein can be used to diagnose
pathogen infections, for example infections by intracellular
bacteria and viruses, by determining the presence and/or quantity
of markers of bacterium or virus, respectively, in the sample.
[00122] A wide variety of infectious diseases can be detected by
the process of the present disclosure. The infectious diseases can
he caused by bacterial, viral, parasite, and fungal infectious
agents. The resistance of various infectious agents to drugs can
also be determined using the present disclosure.
[00123] Bacterial infectious agents which can be detected by the
present disclosure include Escherichia coil, Salmonella, Shigella,
ElESBiella, Pseudomonas, Listeria monocytogenes, Mycobacterium
tuberculosis, Mycobacterium aviumintracellulare, Yersinia,
Francisella, Pasteurella, Brucella, Clostridia, Bordetella
pertussis, Bacteroides, Staphylococcus aureus, Streptococcus
pneumonia, B-Remolytic strep., Corynebacteria, Legionella,
Mycoplasma, Ureaplasma, Chlamydia, Neisseria gonorrhea, Neisseria
meningitides, Hemophilus influenza, Enterococcus faecalis, Proteus
vulgaris, Proteus mirabilis, Relicobacter pylori, Traponema
palladium, Borrelia burgdorferi, Borrelia recurrentis, Rickettsial
pathogens, Nocardia, and Acitnomyretes.
Date Recue/Date Received 2023-08-15
[00124] Fungal infectious agents which can be detected by the
present disclosure include Cryptococcus neoformans, Blastomyces
dermatitidis, Histoplasma capsulatum, Coccidioides immitis,
Paracoccidioides brasiliensis, Candida albicans, Aspergillus
fumigautus, Phycomycetes (Rhizopus), Sporothrix schenckii,
Chromomycosis, and Pladuramycosis.
[00125] Viral infectious agents which can be detected by the
present disclosure include human immunodeficiency virus, human T-
cell lymphocytotrophic virus, hepatitis viruses (e.g., Hepatitis B
Virus and Hepatitis C Virus), Epstein - Barr virus,
cytomegalovirus, human papillomaviruses, orthomyxo viruses,
paramyxo viruses, adenoviruses, corona viruses, rhabdo viruses,
polio viruses, toga viruses, bunya viruses, arena viruses, rubella
viruses, and reo viruses.
[00126] Parasitic agents which can be detected by the present
disclosure include Plasmodium falciparum, Plasmodium malaria,
Plasmodium vivax, Plasmodium ovale, Onchoverva volvulus,
Leishmania, Trypanosoma spp., Schistosoma spp., Entamoeba
histolytica, Cryptosporidum, Giardia spp., Trichimonas spp.,
Balatidium coli, Wuchereria bancrofti, Toxoplasma spp., Enterobius
vermicularis, Ascaris lumbricoides, Trichuris trichiura,
Dracunculus medinesis, trematodes, Diphyllobothrium latum, Taenia
app., Pneumocystis carinii, and Necator americanis.
[00127] The present disclosure is also useful for detection of
drug resistance by infectious agents. For example, vancomycin-
resistant Enterococcus faecium, methicillin-resistant
Staphylococcus aureus, penicillin-resistant Streptococcus
pneumoniae, multi-drug resistant Mycobacterium tuberculosis, and
AZT-resistant human immunodeficiency virus can all be identified
with the present disclosure
[00120] Thus, the target molecules detected using the
compositions and methods of the disclosure can be either patient
markers (such as a cancer marker) or markers of infection with a
foreign agent, such as bacterial or viral markers.
[00129] The compositions and methods of the disclosure can be
used to identify and/or quantify a target molecule whose abundance
is indicative of a biological state or disease condition, for
Date Recue/Date Received 2023-08-15
example, blood markers that are upregulated or downregulated as a
result of a disease state.
[00130] In some embodiments, the methods and compositions of the
present disclosure can be used for cytokine expression. The low
sensitivity of the methods described herein would be helpful for
early detection of cytokines, e.g., as biomarkers of a condition,
diagnosis or prognosis of a disease such as cancer, and the
identification of subclinical conditions.
[00131] The different samples from which the target
polynucleotides are derived can comprise multiple samples from the
same individual, samples from different individuals, or
combinations thereof. In some embodiments, a sample comprises a
plurality of polynucleotides from a single individual. In some
embodiments, a sample comprises a plurality of polynucleotides from
two or more individuals. An individual is any organism or portion
thereof from which target polynucleotides can be derived, non-
limiting examples of which include plants, animals, fungi,
protists, monerans, viruses, mitochondria, and chloroplasts. Sample
polynucleotides can be isolated from a subject, such as a cell
sample, tissue sample, or organ sample derived therefrom,
including, for example, cultured cell lines, biopsy, blood sample,
or fluid sample containing a cell. The subject may be an animal,
including but not limited to, an animal such as a cow, a pig, a
mouse, a rat, a chicken, a cat, a dog, etc., and is usually a
mammal, such as a human. Samples can also be artificially derived,
such as by chemical synthesis. In some embodiments, the samples
comprise DNA. In some embodiments, the samples comprise genomic
DNA. In some embodiments, the samples comprise mitochondrial DNA,
chloroplast DNA, plasmid DNA, bacterial artificial chromosomes,
yeast artificial chromosomes, oligonucleotide tags, or combinations
thereof. In some embodiments, the samples comprise DNA generated by
primer extension reactions using any suitable combination of
primers and a DNA polymerase, including but not limited to
polymerase chain reaction (PCR), reverse transcription, and
combinations thereof. Where the template for the primer extension
reaction is RNA, the product of reverse transcription is referred
to as complementary DNA (cDNA). Primers useful in primer extension
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Date Recue/Date Received 2023-08-15
reactions can comprise sequences specific to one or more targets,
random sequences, partially random sequences, and combinations
thereof. Reaction conditions suitable for primer extension
reactions are known in the art. In general, sample polynucleotides
comprise any polynucleotide present in a sample, which may or may
not include target polynucleotides.
[00132] In some embodiments, nucleic acid template molecules
(e.g., DNA or RNA) are isolated from a biological sample containing
a variety of other components, such as proteins, lipids and non-
template nucleic acids. Nucleic acid template molecules can be
obtained from any cellular material, obtained from an animal,
plant, bacterium, fungus, or any other cellular organism.
Biological samples for use in the present disclosure include viral
particles or preparations. Nucleic acid template molecules can be
obtained directly from an organism or from a biological sample
obtained from an organism, e.g., from blood, urine, cerebrospinal
fluid, seminal fluid, saliva, sputum, stool and tissue. Any tissue
or body fluid specimen may be used as a source for nucleic acid for
use in the disclosure. Nucleic acid template molecules can also be
isolated from cultured cells, such as a primary cell culture or a
cell line. The cells or tissues from which template nucleic acids
are obtained can be infected with a virus or other intracellular
pathogen. A sample can also be total RNA extracted from a
biological specimen, a a/NA library, viral, or genomic DNA. A
sample may also be isolated DNA from a non-cellular origin, e.g.
amplified/isolated DNA from the freezer.
[00133] Methods for the extraction and purification of nucleic
acids are well known in the art. For example, nucleic acids can be
purified by organic extraction with phenol,
phenolichloroform/isoamyl alcohol, or similar formulations,
including TRIzol and TriReagent. Other non-limiting examples of
extraction techniques include: (1) organic extraction followed by
ethanol precipitation, e.g., using a phenol/chloroform organic
reagent (Ausubel et al., 1993), with or without the use of an
automated nucleic acid extractor, e.g., the Model 341 DNA Extractor
available from Applied Biosystems (Foster City, Calif.); (2)
stationary phase adsorption methods (U.S. Pat. No. 5,234,809; Walsh
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Date Recue/Date Received 2023-08-15
et al., 1991); and (3) salt-induced nucleic acid precipitation
methods (Miller et al., (1988), such precipitation methods being
typically referred to as "salting-out" methods. Another example of
nucleic acid isolation and/or purification includes the use of
magnetic particles to which nucleic acids can specifically or non-
specifically bind, followed by isolation of the beads using a
magnet, and washing and eluting the nucleic acids from the beads
(see e.g. U.S. Pat. No. 5,705,628). In some embodiments, the above
isolation methods may be preceded by an enzyme digestion step to
help eliminate unwanted protein from the sample, e.g., digestion
with proteinase K, or other like proteases. See, e.g., U.S. Pat.
No. 7,001,724. If desired, RNase inhibitors may be added to the
lysis buffer. For certain cell or sample types, it may be desirable
to add a protein denaturation/digestion step to the protocol.
Purification methods may be directed to isolate DNA, RNA, or both.
When both DNA and RNA are isolated together during or subsequent to
an extraction procedure, further steps may be employed to purify
one or both separately from the other. Sub-fractions of extracted
nucleic acids can also be generated, for example, purification by
size, sequence, or other physical or chemical characteristic. In
addition to an initial nucleic isolation step, purification of
nucleic acids can be performed after any step in the methods of the
disclosure, such as to remove excess or unwanted reagents,
reactants, or products.
[00134] Nucleic acid template molecules can be obtained as
described in U.S. Patent Application Publication Number
US2002/0190663 Al, published Oct. 9, 2003. Generally, nucleic acid
can be extracted from a biological sample by a variety of
techniques such as those described by Maniatis, et al., Molecular
Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y., pp. 280-281
(1982). In some cases, the nucleic acids can be first extract from
the biological samples and then cross-linked in vitro. In some
cases, native association proteins (e.g. histones) can be further
removed from the nucleic acids.
[00235] In other embodiments, the disclosure can be easily
applied to any high molecular weight double stranded DNA including,
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Date Recue/Date Received 2023-08-15
for example, DNA isolated from tissues, cell culture, bodily
fluids, animal tissue, plant, bacteria, fungi, viruses, etc.
1001361In some embodiments, each of the plurality of independent
samples can independently comprise at least about 1 ng, 2 ng ,5 ng,
ng, 20 ng, 30 ng, 40 ng, 50 ng, 75 ng, 100 ng, 150 ng, 200 ng,
250 ng, 300 ng, 400 ng, 500 ng, 1 pg, 1.5 pg, 2 pg, 5 pg, 10 pg, 20
pg, 50 pg, 100 pg, 200 pg, 500 pg, or 1000 pg, or more of nucleic
acid material. In some embodiments, each of the plurality of
independent samples can independently comprise less than about 1
ng, 2 ng, 5ng, 10 ng, 20 ng, 30 ng, 40 ng, 50 ng, 75 ng, 100 ng,
150 ng, 200 ng, 250 ng, 300 ng, 400 ng, 500 ng, 1 pg, 1.5 pg, 2 pg,
5 pg, 10 pg, 20 pg, 50 pg, 100 pg, 200 pg, 500 pg, or 1000 pg, or
more of nucleic acid.
[002371 In some embodiments, end repair is performed to generate
blunt end 5' phosphorylated nucleic acid ends using commercial
kits, such as those available from Epicentre Biotechnologies
(Madison, WI).
[00136] An adapter oligonucleotide includes any oligonucleotide
having a sequence, at least a portion of which is known, that can
be joined to a target polynucleotide. Adapter oligonucleotides can
comprise DNA, RNA, nucleotide analogues, non-canonical nucleotides,
labeled nucleotides, modified nucleotides, or combinations thereof.
Adapter oligonucleotides can be single-stranded, double-stranded,
or partial duplex. In general, a partial-duplex adapter comprises
one or more single-stranded regions and one or more double-stranded
regions. Double-stranded adapters can comprise two separate
oligonucleotides hybridized to one another (also referred to as an
"oligonucleotide duplex"), and hybridization may leave one or more
blunt ends, one or more 3' overhangs, one or more 5' overhangs, one
or more bulges resulting from mismatched and/or unpaired
nucleotides, or any combination of these. In some embodiments, a
single-stranded adapter comprises two or more sequences that are
able to hybridize with one another. When two such hybridizable
sequences are contained in a single-stranded adapter, hybridization
yields a hairpin structure (hairpin adapter). When two hybridized
regions of an adapter are separated from one another by a non-
hybridized region, a "bubble" structure results. Adapters
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Date Recue/Date Received 2023-08-15
comprising a bubble structure can consist of a single adapter
oligonucleotide comprising internal hybridizations, or may comprise
two or more adapter oligonucleotides hybridized to one another.
Internal sequence hybridization, such as between two hybridizable
sequences in an adapter, can produce a double-stranded structure in
a single-stranded adapter oligonucleotide. Adapters of different
kinds can be used in combination, such as a hairpin adapter and a
double-stranded adapter, or adapters of different sequences.
Hybridizable sequences in a hairpin adapter may or may not include
one or both ends of the oligonucleotide. When neither of the ends
are included in the hybridizable sequences, both ends are "free" or
"overhanging." When only one end is hybridizable to another
sequence in the adapter, the other end forms an overhang, such as a
3' overhang or a 5' overhang. When both the 5'-terminal nucleotide
and the 3'-terminal nucleotide are included in the hybridizable
sequences, such that the 5'-terminal nucleotide and the 3'-terminal
nucleotide are complementary and hybridize with one another, the
end is referred to as "blunt." Different adapters can be joined to
target polynucleotides in sequential reactions or simultaneously.
For example, the first and second adapters can be added to the same
reaction. Adapters can be manipulated prior to combining with
target polynucleotides. For example, terminal phosphates can be
added or removed.
[00239] Adapters can contain one or more of a variety of
sequence elements, including but not limited to, one or more
amplification primer annealing sequences or complements thereof,
one or more sequencing primer annealing sequences or complements
thereof, one or more barcode sequences, one or more common
sequences shared among multiple different adapters or subsets of
different adapters, one or more restriction enzyme recognition
sites, one or more overhangs complementary to one or more target
polynucleotide overhangs, one or more probe binding sites (e.g. for
attachment to a sequencing platform, such as a flow cell for
massive parallel sequencing, such as developed by Illumina, Inc.),
one or more random or near-random sequences (e.g. one or more
nucleotides selected at random from a set of two or more different
nucleotides at one or more positions, with each of the different
46-
Date Recue/Date Received 2023-08-15
nucleotides selected at one or more positions represented in a pool
of adapters comprising the random sequence), and combinations
thereof. Two or more sequence elements can be non-adjacent to one
another (e.g. separated by one or more nucleotides), adjacent to
one another, partially overlapping, or completely overlapping. For
example, an amplification primer annealing sequence can also serve
as a sequencing primer annealing sequence. Sequence elements can be
located at or near the 3' end, at or near the 5' end, or in the
interior of the adapter oligonucleotide. When an adapter
oligonucleotide is capable of forming secondary structure, such as
a hairpin, sequence elements can be located partially or completely
outside the secondary structure, partially or completely inside the
secondary structure, or in between sequences participating in the
secondary structure. For example, when an adapter oligonucleotide
comprises a hairpin structure, sequence elements can be located
partially or completely inside or outside the hybridizable
sequences (the "stem"), including in the sequence between the
hybridizable sequences (the "loop"). In some embodiments, the first
adapter oligonucleotides in a plurality of first adapter
oligonucleotides having different barcode sequences comprise a
sequence element common among all first adapter oligonucleotides in
the plurality. In some embodiments, all second adapter
oligonucleotides comprise a sequence element common among all
second adapter oligonucleotides that is different from the common
sequence element shared by the first adapter oligonucleotides. A
difference in sequence elements can be any such that at least a
portion of different adapters do not completely align, for example,
due to changes in sequence length, deletion or insertion of one or
more nucleotides, or a change in the nucleotide composition at one
or more nucleotide positions (such as a base change or base
modification). In some embodiments, an adapter oligonucleotide
comprises a 5' overhang, a 3' overhang, or both that is
complementary to one or more target polynucleotides. Complementary
overhangs can be one or more nucleotides in length, including but
not limited to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
or more nucleotides in length. For example, the complementary
overhangs can be about 1, 2, 3, 4, 5 or 6 nucleotides in length.
Date Recue/Date Received 2023-08-15
Complementary overhangs may comprise a fixed sequence.
Complementary overhangs may comprise a random sequence of one or
more nucleotides, such that one or more nucleotides are selected at
random from a set of two or more different nucleotides at one or
more positions, with each of the different nucleotides selected at
one or more positions represented in a pool of adapters with
complementary overhangs comprising the random sequence. In some
embodiments, an adapter overhang is complementary to a target
polynucleotide overhang produced by restriction endonuclease
digestion. In some embodiments, an adapter overhang consists of an
adenine or a thymine.
[00140] Adapter oligonucleotides can have any suitable length,
at least sufficient to accommodate the one or more sequence
elements of which they are comprised. In some embodiments, adapters
are about, less than about, or more than about 10, 15, 20, 25, 30,
35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 90, 100, 200, or more
nucleotides in length. In some examples, the adaptors can be about
to about 50 nucleotides in length. In further examples, the
adaptors can be about 20 to about 40 nucleotides in length.
[00141] As used herein, the term "barcode" refers to a known
nucleic acid sequence that allows some feature of a polynucleotide
with which the barcode is associated to be identified. In some
embodiments, the feature of the polynucleotide to be identified is
the sample from which the polynucleotide is derived. In some
embodiments, barcodes can be at least 3, 4, 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, or more nucleotides in length. For example,
barcodes can be at least 10, 11, 12, 13, 14, or 15 nucleotides in
length. In some embodiments, barcodes can be shorter than 10, 9, 8,
7, 6, 5, or 4 nucleotides in length. For example, barcodes can be
shorter than 10 nucleotides in length. In some embodiments,
barcodes associated with some polynucleotides are of different
length than barcodes associated with other polynucleotides. In
general, barcodes are of sufficient length and comprise sequences
that are sufficiently different to allow the identification of
samples based on barcodes with which they are associated. In some
embodiments, a barcode, and the sample source with which it is
associated, can be identified accurately after the mutation,
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Date Recue/Date Received 2023-08-15
insertion, or deletion of one or more nucleotides in the barcode
sequence, such as the mutation, insertion, or deletion of 1, 2, 3,
4, 5, 6, 7, 8, 9, 10, or more nucleotides. In some examples, 1, 2
or 3 nucleotides can be mutated, inserted and/or deleted. In some
embodiments, each barcode in a plurality of barcodes differ from
every other barcode in the plurality at least two nucleotide
positions, such as at least 2, 3, 4, 5, 6, 7, 8, 9, 10, or more
positions. In some examples, each barcode can differ from every
other barcode by in at least 2, 3, 4 or 5 positions. In some
embodiments, both a first site and a second site comprise at least
one of a plurality of barcode sequences. In some embodiments,
barcodes for second sites are selected independently from barcodes
for first adapter oligonucleotides. In some embodiments, first
sites and second sites having barcodes are paired, such that
sequences of the pair comprise the same or different one or more
barcodes. In some embodiments, the methods of the disclosure
further comprise identifying the sample from which a target
polynucleotide is derived based on a barcode sequence to which the
target polynucleotide is joined. In general, a barcode may comprise
a nucleic acid sequence that when joined to a target polynucleotide
serves as an identifier of the sample from which the target
polynucleotide was derived.
[00142] In eukaryotes, genomic DNA is packed into chromatin to
consist as chromosomes within the nucleus. The basic structural
unit of chromatin is the nucleosome, which consists of 146 base
pairs (bp) of DNA wrapped around a histone octamer. The histone
octamer consists of two copies each of the core histone H2A-H2B
dimers and 143-H4 dimers. Nucleosomes are regularly spaced along the
DNA in what is commonly referred to as "beads on a string".
[00143] The assembly of core histones and DNA into nucleosomes
is mediated by chaperone proteins and associated assembly factors.
Nearly all of these factors are core histone-binding proteins. Some
of the histone chaperones, such as nucleosome assembly protein-1
(RAP-1), exhibit a preference for binding to histones H3 and 144. It
has also been observed that newly synthesized histones are
acetylated and then subsequently deacetylated after assembly into
chromatin. The factors that mediate histone acetylation or
Date Recue/Date Received 2023-08-15
deacetylation therefore play an important role in the chromatin
assembly process.
[00144] In general, two in vitro methods have been developed for
reconstituting or assembling chromatin. One method is ATP-
independent, while the second is ATP-dependent. The ATP-independent
method for reconstituting chromatin involves the DNA and core
histones plus either a protein like NAP-1 or salt to act as a
histone chaperone. This method results in a random arrangement of
histones on the DNA that does not accurately mimic the native core
nucleosome particle in the cell. These particles are often referred
to as mononucleosomes because they are not regularly ordered,
extended nucleosome arrays and the DNA sequence used is usually not
Longer than 250 bp (Kundu, T. K. et al., Mol. Cell 6: 551-561,
2000). To generate an extended array of ordered nucleosomes on a
greater length of DNA sequence, the chromatin must be assembled
through an ATP-dependent process.
[00145] The ATP-dependent assembly of periodic nucleosome
arrays, which are similar to those seen in native chromatin,
requires the DNA sequence, core histone particles, a chaperone
protein and ATP-utilizing chromatin assembly factors. ACF (ATP-
utilizing chromatin assembly and remodeling factor) or RSP
(remodeling and spacing factor) are two widely researched assembly
factors that are used to generate extended ordered arrays of
nucleosomes into chromatin in vitro (Pyodorov, D.V., and Kadonaga,
J.T. Method Enzymol. 371: 499-515, 2003; Kundu, T. K. et al. Mol.
Cell 6: 551-561, 2000).
[00146] In particular embodiments, the methods of the disclosure
can be easily applied to any type of fragmented double stranded DNA
including but not limited to, for example, free DNA isolated from
plasma, serum, and/or urine; apoptotic DNA from cells and/or
tissues; DNA fragmented enzymatically in vitro (for example, by
DNase I and/or restriction endonuclease); and/or DNA fragmented by
mechanical forces (hydro-shear, sonication, nebulization, etc.).
[00147] Nucleic acid obtained from biological samples can be
fragmented to produce suitable fragments for analysis. Template
nucleic acids may be fragmented or sheared to desired length, using
a variety of mechanical, chemical and/or enzymatic methods. DNA
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Date Recue/Date Received 2023-08-15
may be randomly sheared via sonication, e.g. Covaris method, brief
exposure to a DNase, or using a mixture of one or more restriction
enzymes, or a transposase or nicking enzyme. RNA may be fragmented
by brief exposure to an RNase, heat plus magnesium, or by shearing.
The RNA may be converted to cDNA. If fragmentation is employed,
the RNA may be converted to cDNA before or after fragmentation. In
some embodiments, nucleic acid from a biological sample is
fragmented by sonication. In other embodiments, nucleic acid is
fragmented by a hydroshear instrument. Generally, individual
nucleic acid template molecules can be from about 2 kb bases to
about 40 kb. In various embodiments, nucleic acids can be about
6kb-10 kb fragments. Nucleic acid molecules may be single-
stranded, double-stranded, or double-stranded with single-stranded
regions (for example, stem- and loop-structures).
[00148] In some embodiments, cross-linked DNA molecules may be
subjected to a size selection step. Size selection of the nucleic
acids may be performed to cross-linked DNA molecules below or above
a certain size. Size selection may further be affected by the
frequency of cross-links and/or by the fragmentation method, for
example by choosing a frequent or rare cutter restriction enzyme.
In some embodiments, a composition may be prepared comprising
cross-linking a DNA molecule in the range of about 1kb to 5 Mb,
about 5kh to 5 Mb, about 5 kB to 2Mb, about 10 kb to 2Mb, about 10
kb to 1 Mb, about 20 kb to 1 Mb about 20 kb to 500 kb, about 50 kb
to 500 kb, about 50 kb to 200 kb, about 60 kb to 200 kb, about 60
kb to 150 kb, about 80 kb to 150 kb, about 80 kb to 120 kb, or
about 100 kb to 120 kb, or any range bounded by any of these values
(e.g. about 150 kb to 1 Mb).
[00149] In some embodiments, sample polynucleotides are
fragmented into a population of fragmented DNA molecules of one or
more specific size range(s). In some embodiments, fragments can be
generated from at least about 1, about 2, about 5, about 10, about
20, about 50, about 100, about 200, about 500, about 1000, about
2000, about 5000, about 10,000, about 20,000, about 50,000, about
100,000, about 200,000, about 500,000, about 1,000,000, about
2,000,000, about 5,000,000, about 10,000,000, or more genome-
equivalents of starting DNA. Fragmentation may be accomplished by
Date Recue/Date Received 2023-08-15
methods known in the art, including chemical, enzymatic, and
mechanical fragmentation. In some embodiments, the fragments have
an average length from about 10 to about 10,000, about 20,000,
about 30,000, about 40,000, about 50,000, about 60,000, about
70,000, about 80,000, about 90,000, about 100,000, about 150,000,
about 200,000, about 300,000, about 400,000, about 500,000, about
600,000, about 700,000, about 800,000, about 900,000, about
1,000,000, about 2,000,000, about 5,000,000, about 10,000,000, or
more nucleotides. In some embodiments, the fragments have an
average length from about 1 kb to about 10 Mb. In some embodiments,
the fragments have an average length from about lkb to 5 Mb, about
5kb to 5 Mb, about 5 kB to 2Mb, about 10 kb to 2Mb, about 10 kb to
1 Mb, about 20 kb to 1 Mb about 20 kb to 500 kb, about 50 kb to 500
kb, about 50 kb to 200 kb, about 60 kb to 200 kb, about 60 kb to
150 kb, about 80 kb to 150 kb, about 80 kb to 120 kb, or about 100
kb to 120 kb, or any range bounded by any of these values (e.g.
about 60 to 120 kb). In some embodiments, the fragments have an
average length less than about 10 Mb, less than about 5 Mb, less
than about 1 Mb, less than about 500 kb, less than about 200 kb,
less than about 100 kb, or less than about 50 kb. In other
embodiments, the fragments have an average length more than about 5
kb, more than about 10 kb, more than about 50 kb, more than about
100 kb, more than about 200 kb, more than about 500 kb, more than
about 1 Mb, more than about 5 Mb, or more than about 10 Mb. In some
embodiments, the fragmentation is accomplished mechanically
comprising subjection sample DNA molecules to acoustic sonication.
In some embodiments, the fragmentation comprises treating the
sample DNA molecules with one or more enzymes under conditions
suitable for the one or more enzymes to generate double-stranded
nucleic acid breaks. Examples of enzymes useful in the generation
of DNA fragments include sequence specific and non-sequence
specific nucleases. Non-limiting examples of nucleases include
DNase I, Fragmentase, restriction endonucleases, variants thereof,
and combinations thereof. For example, digestion with DNase I can
induce random double-stranded breaks in DNA in the absence of Mg44
and in the presence of Mn". In some embodiments, fragmentation
comprises treating the sample DNA molecules with one or more
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Date Recue/Date Received 2023-08-15
restriction endonucleases. Fragmentation can produce fragments
having 5' overhangs, 3' overhangs, blunt ends, or a combination
thereof. In some embodiments, such as when fragmentation comprises
the use of one or more restriction endonucleases, cleavage of
sample DNA molecules leaves overhangs having a predictable
sequence. In some embodiments, the method includes the step of size
selecting the fragments via standard methods such as column
purification or isolation from an agarose gel.
[00150] In some embodiments, the 5' and/or 3' end nucleotide
sequences of fragmented DNA are not modified prior to ligation. For
example, fragmentation by a restriction endonuclease can be used to
leave a predictable overhang, followed by ligation with a nucleic
acid end comprising an overhang complementary to the predictable
overhang on a DNA fragment. In another example, cleavage by an
enzyme that leaves a predictable blunt end can be followed by
ligation of blunt-ended DNA fragments to nucleic acids, such as
adapters, oligonucleotides, or polynucleotides, comprising a blunt
end. In some embodiments, the fragmented DNA molecules are blunt-
end polished (or "end repaired") to produce DNA fragments having
blunt ends, prior to being joined to adapters. The blunt-end
polishing step may be accomplished by incubation with a suitable
enzyme, such as a DNA polymerase that has both 3' to 5' exonuclease
activity and 5' to 3' polymerase activity, for example T4
polymerase. In some embodiments, end repair can be followed by an
addition of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20 or more nucleotides, such as one or more adenine,
one or more thymine, one or more guanine, or one or more cytosine,
to produce an overhang. For example, the end pair can be followed
by an addition of 1, 2, 3, 4, 5, or 6 nucleotides. DNA fragments
having an overhang can be joined to one or more nucleic acids, such
as oligonculeotides, adapter oligonucleotides, or polynucleotides,
having a complementary overhang, such as in a ligation reaction.
For example, a single adenine can be added to the 3' ends of end
repaired DNA fragments using a template independent polymerase,
followed by ligation to one or more adapters each having a thymine
at a 3' end. In some embodiments, nucleic acids, such as
oligonucleotides or polynucleotides can be joined to blunt end
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Date Recue/Date Received 2023-08-15
double-stranded DNA molecules which have been modified by extension
of the 3 end with one or more nucleotides followed by 5'
phosphorylation. In some cases, extension of the 3' end may be
performed with a polymerase such as, Klenow polymerase or any of
the suitable pclymerases provided herein, or by use of a terminal
deoxvnucleotide transferase, in the presence of one or more dNTPs
in a suitable buffer that can contain magnesium. In some
embodiments, target polynncleotides having blunt ends are joined to
one or more adapters comprising a blunt end. Phospherylation of 5'
ends of DNA fragment molecules may be performed for example with T4
polynucleotide kinase in a suitable buffer containing ATP and
magnesium. The fragmented DNA molecules may optionally be treated
to dephosphorylate 5' ends or 3' ends, for example, by using
en2ymes known in the art, such as phosphatases.
[00151] The terms "connecting, ''.joining" and "ligation'? as used
herein, with respect to two polynucleotides, such as an adapter
oligonucleotide and a target polynuclectide, refers to the covalent
attachment of two separate DNA segments to produce a single larger
polynucleotide with a contiguous backbone. Methods for joiniag two
DNA segments are known in the art, and include without limitation,
enzymatic and non-enzymatic (e.g. chemical) methods. Examples of
ligation reactions that are non-enzymatic include the non-enzymatic
ligation techniques described in U.S. Pat. Nos. 5,780,613 and
5,476,930. In some
embodiments, an adapter oligoeucleotide is joined to a target
polynucleotide by a ligase, for example a DNA ligase ox RNA ligase.
Multiple ligases, each having characterized reaction conditions,
are known in the art, and include, without limitation WAD'-
dependent ligases including tRNA ligase, Tag DNA ligase, Thermus
filiformis DNA ligase, Escherichia colj DNA ligase, Tth DNA ligase,
Thermus scotoductus DNA ligase (I and 21), thermostable ligase,
Ampligase thermostable DNA ligase, VanC-type ligase, 9 N DNA
Ligase, Tsp DNA ligase, and novel linases discovered by
bioproepecting; ATP-dependent ligases including T4 RNA ligase, T4
DNA ligase, Tl DNA ligase, T7 DNA ligase, Pfu DNA ligase, DNA
ligase I, DNA. Aigase ITT, DNA ligase IV, and novel ligases
Date Recue/Date Received 2023-08-15
discovered by bioprospectina; and wild-type, mutant isoforms, and
genetically engineered variants thereof.
[00152] Ligation can be between DINA segments having hybridizable
sequences, such as complementary overhangs. Ligation can also he
between two blunt ends. Generally, a 5' phosphate is utilized in a
ligation reaction. The 5' phosphate can be provided by the target
polynucleotide, the adapter oligonucleotide, or both. 5' phosphates
can be added to or removed from DNA segments to he joined, as
needed. Methods for the addition or removal of 5' phosphates are
known in the art, and include without limitation enzymatic and
chemical processes. Enzymes useful in the addition andlor removal
of 5' phosphates include kinases, phosphatases, and polymerases. In
some embodiments, both of the two ends joined in a ligation
reaction (e.g. an adapter end and a target polynucleotide end)
provide a 5' phosphate, such that two covalent linkages are made in
joining the two ends. In some embodiments, only one of the two ends
joined in a ligation reaction (e.g. only one of an adapter end and
a target polynucleotide end) provides a 5' phosphate, such that
only one covalent linkage is made in joining the two ends.
[00153] In some embodiments, only one strand at one or both ends
of a target polynucleotide is joined to an adapter o].igonucleotide.
In some embodiments, both strands at one or both ends of a target
polynucleotide are joined to an adapter oligonucleotide. In some
embodiments, 3' phosphates are removed prior to ligation. In some
embodiments, an adapter oligonucleotide is added to both ends of a
target polynucleotide, wherein one or both strands at each end are
joined to one or more adapter oligonucleotides. When both strands
at both ends are joined to an adapter oligonucleotide, joining can
be followed by a cleavage reaction that leaves a 5' overhang that
can serve as a template for the extension of the corresponding 3'
end, which 3' end may or may not include one or more nucleotides
derived from the adapter oligonucleotide. In some embodiments, a
target polynucleotide is joined to a first adapter oligonucleotide
on one end and a second adapter oligonucleotide on the other end.
In some embodiments, two ends of a target polynucleotide are joined
to the opposite ends of a single adapter oligonucleotide. In some
embodiments, the target polynucleotide and the adapter
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Date Recue/Date Received 2023-08-15
oligonucleotide to which it is joined comprise blunt ends. In some
embodiments, separate ligation reactions can be carried out for
each sample, using a different first adapter oligonucleotide
comprising at least one barcode sequence for each sample, such that
no barcode sequence is joined to the target polynucleotides of more
than one sample. A DNA segment or a target polynucleotide that has
an adapter oligonuclectide joined to it is considered "tagged' by
the joined adapter.
[00154] In some cases, the ligation reaction can be performed at
a DNA segment or target polynucleotide concentration of about 0.1
ng/pL, about 0.2 ng/pL, about 0.3 ng/pL, about 0.4 ng/pL, about 0.5
ng/pL, about 0.6 ng/pL, about 0.7 ng/pL, about 0.8 ng/pL, about 0.9
ng/pL, about 1.0 ng/pL, about 1.2 ng/pL, about 1.4 ng/pL, about 1.6
ng/pL, about 1.8 ng/pL, about 2.0 ng/gL, about 2.5 ng/gL, about 3.0
ng/pL, about 3.5 ng/pL, about 4.0 ng/gL, about 4.5 ng/gL, about 5.0
ng/pL, about 6.0 ng/pL, about 7.0 ng/pL, about 8.0 ng/pL, about 9.0
ng/pL, about 10 ng/pL, about 15 ng/pL, about 20 ng/pL, about 30
ng/pL, about 40 ng/pL, about 50 ng/pL, about 60 ng/ 1., about 70
ng/pL, about 80 ng/pL, about 90 ng/pL, about 100 ng/pL, about 150
ng/pL, about 200 ng/pL, about 300 ng/pL, about 400 ng/gL, about 500
nq/pL, about 600 nq/pL, about 800 nq/pL, or about 1000 nq/pL. For
example, the ligation can be performed at a DNA segment or target
polynucleotide concentration of about 100 ng/pL, about 150 ng/pL,
about 200 ng/pL, about 300 ng/pL, about 400 ng/pL, or about 500
ng/pL.
[001551 In some cases, the ligation reaction can be performed at
a DNA segment or target polynucleotide concentration of about 0.1
to 1000 ngipL, about 1 to 1000 ng/pL, about 1 to 800 ng/pL, about
to 800 ng/pL, about 10 to 600 ng/ 1., about 100 to 600 ng/pL, or
about 100 to 500 ng/pL.
[001561 In some cases, the ligation reaction can be performed
for more than about 5 minutes, about 10 minutes, about 20 minutes,
about 30 minutes, about 40 minutes, about 50 minutes, about 60
minutes, about 90 minutes, about 2 hours, about 3 hours, about 4
hours, about 5 hours, about 6 hours, about 8 hours, about 10 hours.
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Date Recue/Date Received 2023-08-15
about 12 hours, about 18 hours, about 24 hours, about 36 hours,
About 48 hours, or about 96 hours. In other cases, the ligation
reaction can be performed for less than about 5 minutes, about 10
minutes, about 20 minutes, About 30 minutes, about 40 minutes,
about 50 minutes, about 60 minutes, about 90 minutes, about 2
hours, about 3 hours, about 4 hours, about 5 hours, about 6 hours,
about 8 hours, about 10 hours, about 12 hours, about 18 hours,
about 24 hours, about 36 hours, about 48 hours, or about 96 hours.
For example, the ligation reaction can be performed for about 30
minutes to about 90 minutes. In some embodiments, joining of an
adapter to a target polynucleotide produces a joined product
polynucleotide having a 3' overhang comprising a nucleotide
sequence derived from the adapter.
[00157] In some embodiments, after joining at least one adapter
oligonucleotide to a target polynucleotide, the 3' end of one or
more target polynucleotideo is extended using the one or more
joined adapter oligonucleotides as template. For example, an
adapter comprising two hybridized oligonucleotides that is joined
to only the 5' end of a target polynucleotide allows for the
extension of the unjoined 3' end of the target using the joined
strand of the adapter as template, concurrently with or following
displacement of the unjoined strand. Both strands of an adapter
comprising two hybridized oligonucleotides may be joined to a
target polynucleotide such that the joined product has a 5'
overhang, and the complementary 3' end can be extended using the 5'
overhang as template. AS a further example, a hairpin adapter
oligonucleotide can be joined to the 5' end of a target
polynucleotide. In some embodiments, the 3' end of the target
polynucleotide that is extended comprises one or more nucleotides
from an adapter oligonucleotide. For target polynucleotides to
which adapters are joined on both ends, extension can be carried
out for both 3' ends of a double-stranded target polynucleotide
having 5' overhangs. This 3' end extension, or "fill-in" reaction,
generates a complementary sequence, or "complement," to the adapter
oligonucleotide template that Is hybridized to the template, thus
filitvg in the 3' overhang to produce a double-stranded sequence
region. Where both ends of a double-stranded target polynucleotide
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have 5' overhangs that are filled in by extension of the
complementary strands 3' ends, the product is completely double-
stranded. Extension can be carried out by any suitable polymerase
known in the art, such as a DNA polymerase, many of which are
commercially available. DNA polymerases can comprise DNA-dependent
DNA polymexase activity, RIA-dependent DNA polymerase activity, or
DNA-dependent and RNA-dependent DNA polymerase activity. DNA
polymerases can be thermostable or non-thermostabae. Examples of
DNA polymerases include, but are not limited to, Tag polymerase,
Tth polymerase, Tli polymerase, Pfu polymerase, Pfutubo polymerase,
pyrobest polymerase, Pwo polymerase, KOD polymerase, Bst
polymerase, Sac polymerase, Sao polymerase, Poo polymerase, Pah
polymerase, Mth polymerase, Pho polymerase, E54 polymerase, VENT
polymerase, DEEPVENT polymerase, EX-Taq polymerase, Lk-Tag
polymerase, Expand polymerases, Platinum Taq polymerases, Hi-Fl
poivmerase, Tbr polymerase, rfl pelymeraoe, Tru polymerase, Tac
polymerase, Tne polymerase, rma polymerase, Tih polymerase, Tfi
polymerase, Kienow fragment, and variants, modified products and
derivatives thereof 3' end extension can be performed before or
after pooling of target polynucleotides from independent samples.
[00158] In certain embodiments, the disclosure provides methods
for the enrichment of a target nucleic acids and analysis of the
target nucleic acids. In some cases, the methods for enrichment is
in a solution based format. In some cases, the target nucleic acid
can be labeled with a labeling agent. In other cases, the target
nucleic acid can be crosslinked to one or more association
molecules that are labeled with a labeling agent. Examples of
labeling agents include but are not limited to biotin,
polyhistidine tags, and chemical tags (e.g. alkyne and azide
derivatives used in Click Chemistry methods). Further, the labeled
target nucleic acid can be captured and thereby enriched by using a
capturing agent. The capturing agent can be streptavidin and/or
avidin, an antibody, a chemical moiety (e.g. alkyne, azide), and
any biological, chemical, physical, or enzymatic agents used for
affinity purification known in the art.
(001591 In some cases, immobilized or non-immobilized nucleic
acid probes can be used to capture the target nucleic acids. For
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example, the target nucleic acids can be enriched from a sample by
hybridization to the probes on a solid support or in solution. In
SOME examples, the sample can be a genomic sample. In some
examples, the probes can be an amolicon. The amplicon can comprise
a predetermined sequence. Further, the hybridized target nucleic
acids can be washed and/or eluted off of the probes. The target
nucleic acid can be a DNA, RNA, cDNA, or mRNA molecule.
[00160] In some cases, the enrichment method can comprise
contacting the sample comprising the target nucleic acid to the
probes and binding the target nucleic acid tc a solid support. In
some cases, the sample can be fragmented using chemical, physical
or enzymatic methods to yield the target nucleic acids. In some
cases, the probes can be specifically hybridized to the target.
nucleic acids. In some cases, the target nucleic acids can have an
average size of about 50 to 5000, about 50 to 2000, about 100 to
2000, about 100 to 1000, about 200 to 1000, about 200 to 800, or
about 300 to 800, about 300 to 600, or about 400 to 600 nucleotide
residues. The target nucleic acids can be further separated from
the unbound nucleic acids in the sample. The solid support can be
washed andior eluted to provide the enriched target nucleic acids.
In some examples, the enrichment steps can be repeated for About 1,
2, 3, 4, 5, 6, 7, 0, 9, or 10 times. For example, the enrichment
steps can be repeated for about 1, 2, or 3 times.
[00161] In some cases, the enrichment method can comprise
providing probe derived amplicons wherein said probes for
amplification are attached to a solid support. The solid support
can comprise support-immobilized nucleic acid probes to capture
specific target nucleic acid from a sample. The probe derived
amplicons can hybridize to the target nucleic acids. Following
hybridization to the probe amplicons, the target nucleic acids in
the sample can be enriched by capturing (e.g., via capturing agents
as biotin, antibodies, etc.) and washing and/or eluting the
hybridized target nucleic acids from the captured probes (FIG. 4).
The target nucleic acid sequence(s) may be further amplified using,
for example, PM methods to produce an amplified pool of enriched
PCR products.
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[00162] In some cases, the solid support can be a microarray, a
slide, a chip, a microwell, a column, a tube, a particle or a bead.
In some examples, the solid support can be coated with streptavidin
and/or avidin. In other examples, the solid support can be coated
with an antibody. Further, the solid support can comprise a glass,
metal, ceramic or polymeric material. In some embodiments, the
solid support can be a nucleic acid microarray (e.g. a DNA
microarray). In other embodiments, the solid support can be a
paramagnetic bead.
[00163] In some cases, the enrichment method can comprise
digestion with a secondary restriction enzyme, self-ligation (e.g.
self-circularization), and re-digestion with the original
restriction enzyme. In particular examples, only the ligation
products will be linearized and available for adapter-ligation and
sequencing. In other cases, the ligation junction sequence itself
can be used for hybridization based enrichment using a bait-probe
complimentary to the junction sequence.
[00164] In particular embodiments, the disclosure provides
methods for amplifying the enriched DNA. In some cases, the
enriched DNA is a read-pair. The read-pair can be obtained by the
methods of the present disclosure.
[00165] In some embodiments, the one or more amplification
and/or replication steps are used for the preparation of a library
to be sequenced. Any amplification method known in the art may be
used. Examples of amplification techniques that can be used
include, but are not limited to, quantitative PCR, quantitative
fluorescent PCR (U-PCR), multiplex fluorescent PCR (MF-PCR), real
time PCR (RTPCR), single cell PCR, restriction fragment length
polymorphism PCR (PCR-RFLP), PCK-RFLPIRT-PCR-IRFLP, hot start PCR,
nested PCR, in situ polonony PCR, in situ rolling circle
amplification (RCA), bridge PCR , ligation mediated PCR, Qb
replicase dmplificAion, inver6e PCR, picotiter PCR and emulsion
PCR. Other suitable amplification methods include the ligase chain
reaction (LCR), transcription amplification, self-sustained
sequence replication, selective amplification of target
polynucleotide sequences, consensus sequence primed polymerase
chain reaction (CP-PCR), arbitrarily primed polymerase chain
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reaction (AP-PCR), degenerate oligonucleotide-primed PCR (DOP-PCR)
and nucleic acid based sequence amplification (NABSA). Other
amplification methods that can be used herein include those
described in U.S. Patent Nos. 5,242,794; 5,494,810; 4,988,617; and
6,582,938.
[00166] In particular embodiments, PCR is used to amplify DNA
molecules after they are dispensed into individual partitions. In
some cases, one or more specific priming sequences within
amplification adapters are utilized for PCR amplification. The
amplification adapters may be ligated to fragmented DNA molecules
before or after dispensing into individual partitions.
Polynucleotides comprising amplification adapters with suitable
priming sequences on both ends can be PCR amplified exponentially.
Polynucleotides with only one suitable priming sequence due to, for
example, imperfect ligation efficiency of amplification adapters
comprising priming sequences, may only undergo linear
amplification. Further, polynucleotides can be eliminated from
amplification, for example PCR amplification, all together, if no
adapters comprising suitable priming sequences are ligated. In some
embodiments, the number of PCR cycles vary between 10-30, but can
be as low as 9, 8, 7, 6, 5, 4, 3, 2 or less or as high as 40, 45,
50, 55, 60 or more. As a result, exponentially amplifiable
fragments carrying amplification adapters with a suitable priming
sequence can be present in much higher (1000 fold or more)
concentration compared to linearly amplifiable or un-amplifiable
fragments, after a PCR amplification. Benefits of PCR, as compared
to whole genome amplification techniques (such as amplification
with randomized primers or Multiple Displacement Amplification
using ph129 polymerase) include, but are not limited to a more
uniform relaLive sequence coverage - as each fragment_ can be copied
at most once per cycle and as the amplification is controlled by
thermocycling program, a substantially lower rate of forming
chimeric molecules than for example MDA (Lasken et al., 2007, BMC
Biotechnology) - as chimeric molecules pose significant challenges
for accurate sequence assembly by presenting nonbiological
sequences in the assembly graph, which may result in higher rate of
misassemblies or highly ambiguous and fragmented assembly, reduced
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Date Recue/Date Received 2023-08-15
sequence specific biases that may result from binding of rand0m12ed
primers commonly used in NDA versus using specific priming sites
with a specific sequence, a higher reproducibility in the amount of
final amplified DNA product, which can be controlled by selection
of the number of PCR cycles, and a higher fidelity in replication
with the polymerases that are commonly used in PR as compared to
common whole genome amplification techniques known in the art.
[00167] In some embodiments, the fill-in reaction is followed by
or performed as part of amplification of one or more target
polynucleotides using a first primer and a second primer, wherein
the first primer comprises a sequence that is hybridizable to at
least a portion of the complement of one or more of the first
adapter oligonucleotides, and further wherein the second primer
comprises a sequence that is hybridizable to at least a portion of
the complement of one or more of the second adapter
oligonucleotides. Each of the first and second primers may be of
any suitable length, such as about, less than about, or more than
about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80,
90, 100, or more nucleotides, any portion or all of which may be
complementary to the corresponding target sequence (e.g. about,
less than about, or more than about 5, 10, 15, 20, 25, 30, 35, 40,
45, 50, or more nucleotides). For example, about 10 to 50
nucleotides can be complementary to the corresponding target
sequence.
[00168] 'Amplification" refers to any process by which the copy
number of a target sequence is increased. In some cases, ft
replication reaction may produce only a single complementary
copy/replica of a polynucleotide. Eethods for primer-directed
amplification of target polynucleotides are known in the art, and
include without limitation, methods based on the polymerase chain
reaction (PCR). Conditions favorable to the amplification of target
sequences by PR are known in the art, can be optimized at a
variety of steps in the process, and depend on characteristics of
elements in the reaction, such as target type, target
concentration, sequence length to be amplified, sequence of the
target and/or one or more primers, primer length, primer
concentration, polymerase used, reaction volume, ratio of one or
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more elements to one or more other elements, and others, some or
all of which can be altered. In general, PCR involves the steps of
denaturation of the target to be amplified (if double stranded),
hybridization of one or more primers to the target, and extension
of the primers by a DNA polymerase, with the steps repeated (or
"cycled") in order to amplify the target sequence. Steps in this
process can be optimized for various outcomes, such as to enhance
yield, decrease the formation of spurious Products, and/or increase
or decrease specificity of primer annealing. Methods of
optimization are well known in the art and include adjustments to
the type ox amount of elements in the amplification reaction and/or
to the conditions of a given step in the process, such as
temperature at a particular step, duration of a particular step,
and/or number of cycles.
[00169] In some embodiments, an amplification reaction can
comprise at least about 5, 10, 15, 20, 25, 30, 35, 40, 50, 60, 70,
80, 90, 100, 150, 200 or more cycles. In some examples, an
amplification reaction can comprise at least about 20, 25, 30, 35
or 40 cycles. In some embodiments, an amplification reaction
comprises no more than about 5, 10, 15, 20, 25, 35, 40, 50, 60, 70,
80, 90, 100, 150, 200 or more cycles. Cycles can contain any number
of steps, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more steps.
Steps can comprise any temperature or gradient of temperatures,
suitable for achieving the purpose of the given step, including but
not limited to, 3' end extension (e.g. adapter fill-in), primer
annealing, primer extension, and strand denaturation. Steps can be
of any duration, including but not limited to about, less than
about, or more than about 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50,
55, 60, 70, 80, 90, 100, 120, 180, 240, 300, 360, 420, 480, 540,
600, 1200, 1800, or more seconds, including indefinitely until
manually interrupted. Cycles of any number comprising different
steps can be combined in any order. In some embodiments, different
cycles comprising different steps are combined such that the total
number of cycles in the combination is about, less that about, or
more than about 5, 10, 15, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90,
100, 130, 200 or more cycles. In some embodiments, amplification is
performed following the fill-in reaction.
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Date Recue/Date Received 2023-08-15
[001701 In some embodiments, the amplification reaction can be
carried out on at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12,
14, 16, 18, 20, 25, 30, 40, 50, 100, 2CO3 300, 400, 500, 600, 800,
1000 ng of the target DNA molecule. In other embodiments, the
amplification reaction can be carried cut on less than about 1, 2,
3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18, 20, 25, 30, 40, 50, 100,
200, 300, 400, 500, 600, 800, 1000 ng of the target DNA molecule.
[00171] Amplification can be performed before or after pooling
of target polynucleotides from independent samples.
[00172] Methods of the disclosure involve determining an amount
of amplifiable nucleic acid present in a sample. Any known method
may be used to quantify amplifiable nucleic acid, and an exemplary
method is the polymerase chain reaction (PCR), specifically
quantitative polymerase chain reaction (qPCR). qPCR is a technique
based on the polymerase chain reaction, and is used to amplify and
simultaneously quantify a targeted nucleic acid molecule. qPCR
allows for both detection and quantification (as absolute number of
copies or relative amount when normalized to DNA input or
additional normalizing genes) of a specific sequence in a DNA
sample. The procedure follows the general principle of polymerase
chain reaction, with the additional feature that the amplified DNA
is quantified as it accumulates in the reaction in real time after
each amplification cycle. QPCR is described, for example, in
Kurnit et al. (U.S. patent number 6,032,854), Wang et al. (U.S.
patent number 5,567,583 and 5,348,853), Ma et al. (The Journal of
American Science, 2(3), 2006), Heid et al. (Genome Research 986-
994, 1996), Sambrook and Russell (Quantitative PCR, Cold Spring
Harbor Protocols, 2006), and Higuchi (C.S. patent numbers 6,171,785
and 5,994,056).
[00173] Other methods of quantification include use of
fluorescent dyes that intercalate with double-stranded DNA, and
modified DNA oligonucleotide probes that fluoresce when hybridized
with a complementary DNA. These methods can be broadly used but
are also specifically adapted to real-time PCR as described in
further detail as an example. In the first method, a DNA-binding
dye binds to all double-stranded (ds)DNA in PCR, resulting in
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Date Recue/Date Received 2023-08-15
fluorescence of the dye. An increase in DNA product during PCR
therefore leads to an increase in fluorescence intensity and is
measured at each cycle, thus allowing DNA concentrations to be
quantified. The reaction is prepared similarly to a standard PCR
reaction, with the addition of fluorescent (ds)DNA dye. The
reaction is run in a thermocycler, and after each cycle, the levels
of fluorescence are measured with a detector; the dye only
fluoresces when bound to the (ds)DNA (i.e., the PCR product). With
reference to a standard dilution, the (ds)DNA concentration in the
PCR can be determined. Like other real-time PCR methods, the
values obtained do not have absolute units associated with it. A
comparison of a measured DNA/RNA sample to a standard dilution
gives a fraction or ratio of the sample relative to the standard,
allowing relative comparisons between different tissues or
experimental conditions. To ensure accuracy in the quantification
and/or expression of a target gene can be normalized with respect
to a stably expressed gene. Copy numbers of unknown genes can
similarly be normalized relative to genes of known copy number.
[00174] The second method uses a sequence-specific RNA or DNA-
based probe to quantify only the DNA containing a probe sequence;
therefore, use of the reporter probe significantly increases
specificity, and allows quantification even in the presence of some
non-specific DNA amplification. This allows for multiplexing,
i.e., assaying for several genes in the same reaction by using
specific probes with differently colored labels, provided that all
genes are amplified with similar efficiency.
[00175] This method is commonly carried out with a DNA-based
probe with a fluorescent reporter (e.g. 6-carboxyfluorescein) at
one end and a quencher (e.g., 5-carboxy-tetramethylrhodamine) of
fluorescence al. the opposite end of the probe. The close proximity
of the reporter to the quencher prevents detection of its
fluorescence. Breakdown of the probe by the 5' to 3' exonuclease
activity of a polymerase (e.g., Tact polymerase) breaks the
reporter-quencher proximity and thus allows unquenched emission of
fluorescence, which can be detected. An increase in the product
targeted by the reporter probe at each PCR cycle results in a
proportional increase in fluorescence due to breakdown of the probe
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Date Recue/Date Received 2023-08-15
and release of the reporter. The reaction is prepared similarly to
a standard PCR reaction, and the reporter probe is added. As the
reaction commences, during the annealing stage of the PCR both
probe and primers anneal to the DNA target. Polymerization of a
new DNA strand is initiated from the primers, and once the
polymerase reaches the probe, its 5'-3'-exonuclease degrades the
probe, physically separating the fluorescent reporter from the
quencher, resulting in an increase in fluorescence. Fluorescence
is detected and measured in a real-time PCR thermocycler, and
geometric increase of fluorescence corresponding to exponential
increase of the product is used to determine the threshold cycle in
each reaction.
[001761 Relative concentrations of DNA present during the
exponential phase of the reaction are determined by plotting
fluorescence against cycle number on a logarithmic scale (so an
exponentially increasing quantity will give a straight line). A
threshold for detection of fluorescence above background is
determined. The cycle at which the fluorescence from a sample
crosses the threshold is called the cycle threshold, C. Since the
quantity of DNA doubles every cycle during the exponential phase,
relative amounts of DNA can be calculated, e.g. a sample with a Ct
of 3 cycles earlier than another has 23 - 8 times more template.
Amounts of nucleic acid (e.g., RNA or DNA) are then determined by
comparing the results to a standard curve produced by a real-time
PCR of serial dilutions (e.g. undiluted, 1:4, 1:16, 1:64) of a
known amount of nucleic acid.
[00177] In certain embodiments, the qPCR reaction involves a
dual fluorophore approach that takes advantage of fluorescence
resonance energy transfer (FRET), e.g., LIGHTCYCLER hybridization
probes, where two oligonucleotide probes anneal to the amplicon
(e.g. see U.S. patent number 6,174,670). The oliqonucleotides are
designed to hybridize in a head-to-tail orientation with the
fluorophores separated at a distance that is compatible with
efficient energy transfer. Other examples of labeled
oligonucleotides that are structured to emit a signal when bound to
a nucleic acid or incorporated into an extension product include:
SCORPIONS probes (e.g., Whitcombe et al., Nature Biotechnology
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Date Recue/Date Received 2023-08-15
17:804-807, 1999, and U.S. patent number 6,326,145), Sunrise (or
AMPLIFLOUR) primers (e.g., Nazarenko et al., Nuc. Acids Res.
25:2516-2521, 1997, and U.S. patent number 6,117,635), and LUX
primers and MOLECULAR BEACONS probes (e.g., Tyagi et al., Nature
Biotechnology 14:303-308, 1996 and U.S. patent number 5,989,823).
[00178] In other embodiments, a qPCR reaction uses fluorescent
Taqman methodology and an instrument capable of measuring
fluorescence in real time (e.g., ABI Prism 7700 Sequence Detector).
The Tatman reaction uses a hybridization probe labeled with two
different fluorescent dyes. One dye is a reporter dye (6-
carboxyfluorescein), the other is a quenching dye (6-carboxy-
tetramethylrhodamine). When the probe is intact, fluorescent energy
transfer occurs and the reporter dye fluorescent emission is
absorbed by the quenching dye. During the extension phase of the
PCR cycle, the fluorescent hybridization probe is cleaved by the
5'-3' nucleolytic activity of the DNA polymerase. On cleavage of
the probe, the reporter dye emission is no longer transferred
efficiently to the quenching dye, resulting in an increase of the
reporter dye fluorescent emission spectra. Any nucleic acid
quantification method, including real-time methods or single-point
detection methods may be used to quantify the amount of nucleic
acid in the sample. The detection can be performed several
different methodologies (e.g., staining, hybridization with a
labeled probe; incorporation of biotinylated primers followed by
avidin-enzyme conjugate detection; incorporation of 32P-labeled
deoxynucleotide triphosphates, such as dCTP or dATP, into the
amplified segment), as well as any other suitable detection method
known in the art for nucleic acid quantification. The
quantification may or may not include an amplification step.
[00179] In some embodiments, the disclosure provides labels for
identifying or quantifying the linked DNA segments. In some cases,
the linked DNA segments can be labeled in order to assist in
downstream applications, such as array hybridization. For example,
the linked DNA segments can be labeled using random priming or nick
translation.
[00180] A wide variety of labels (e.g. reporters) may be used to
label the nucleotide sequences described herein, including but not
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Date Recue/Date Received 2023-08-15
limited to during the amplification step. Suitable labels include
radionuclides, enzymes, fluorescent, chemiluminescent, or
chromogenic agents as well as ligands, cofactors, inhibitors,
magnetic particles and the like. Examples of such labels are
included in U.S. Pat. No. 3,817,837; U.S. Pat. No. 3,850,752; U.S.
Pat. No. 3,939,350; U.S. Pat. No. 3,996,345; U.S. Pat. No.
4,277,437; U.S. Pat. No. 4,275,149 and U.S. Pat. No. 4,366,241.
[00181] Additional labels include but are not limited to 13-
galactosidase, invertase, green fluorescent protein, luciferase,
chloramphenicol, acetyltransferase, 0-glucuronidase, exo-glucanase
and glucoamylase. Fluorescent labels may also be used, as well as
fluorescent reagents specifically synthesized with particular
chemical properties. A wide variety of ways to measure fluorescence
are available. For example, some fluorescent labels exhibit a
change in excitation or emission spectra, some exhibit resonance
energy transfer where one fluorescent reporter loses fluorescence,
while a second gains in fluorescence, sane exhibit a loss
(quenching) or appearance of fluorescence, while some report
rotational movements.
[00182] Further, in order to obtain sufficient material for
labeling, multiple amplifications may be pooled, instead of
increasing the number of amplification cycles per reaction.
Alternatively, labeled nucleotides can be incorporated in to the
last cycles of the amplification reaction, e.g. 30 cycles of PCR
(no label) +10 cycles of PCR (plus label).
[00183] In particular embodiments, the disclosure provides
probes that can attach to the linked DNA segments. As used herein,
the term 'probe" refers to a molecule (e.g., an oligonucleotide,
whether occurring naturally as in a purified restriction digest or
produced synthetically, recoMbinantly or by PCR amplification),
that is capable of hybridizing to another molecule of interest
(e.g., another oligonucleotide). When probes are oligonucleotides
they may be single-stranded or double-stranded. Probes are useful
in the detection, identification and isolation of particular
targets (e.g., gene sequences). In some cases, the probes may be
associated with a label so that is detectable in any detection
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Date Recue/Date Received 2023-08-15
system, including, but not limited to enzyme (e.g., ELISA, as well
as enzyme-based histochemical assays), fluorescent, radioactive,
and luminescent systems
[00184] With respect to arrays and microarrays, the term "probe"
is used to refer to any hybridizable material that is affixed to
the array for the purpose of detecting a nucleotide sequence that
has hybridized to said probe. In some cases, the probes can about
bp to 500 bp, about 10 bp to 250 bp, about 20 bp to 250 bp,
about 20 bp to 200 bp, about 25 bp to 200 bp, about 25 bp to 100
bp, About 30 bp to 100 bp, or about 30 bp to 80 bp. In some cases,
the probes can be greater than about 10 bp, about 20 bp, about 30
bp, about 40 bp ,about 50 bp, about 60 bp, about 70 bp, about 80
bp, about 90 bp, about 100 bp, about 150 bp, about 200 bp, about
250 bp, about 300 bp, About 400 bp, or about 500 bp in length. For
example, the probes can be about 20 to about 50 bp in length.
Examples and rationale for probe design can be found in W095/11995,
EP 717,113 and W097/29212
[001851 In some cases, one or more probes can be designed such
that they can hybridize close to the sites that are digested by a
restriction enzyme. For example, the probe(s) can be within about
10 bp, about 20 bp, about 30 bp, about 40 bp, About 50 bp, About 60
bp, about 70 bp, about 80 bp, about 90 bp, about 100 bp, about 150
bp, about 200 bp, about 250 bp, about 300 bp, about 400 bp, or
about 500 bp of the restriction enzyme recognition site.
[00186] In other cases, a single, unique, probe can designed
within about 10 bp, about 20 bp, about 30 bp, about 40 bp, about 50
bp, about 60 bp, about 70 bp, about 80 bp, about 90 bp, about 100
bp, about 150 bp, about 200 bp, about 250 bp, about 300 bp, about
400 bp, or about 500 bp at each side of the sites that are digested
by the restriction enzyme. The probes can be designed such that
they can hybridize at either side of the sites that are digested by
the restriction enzyme. For example, a single probe at each side of
the primary restriction enzyme recognition site can be used
(00187] In further cases, 2, 3, 4, 5, 6, 7, 8, or more probes
can be designed at each side of the restriction enzyme recognition
site, which can then be used to investigate the same ligation
event. For example, 2 or 3 probes can be designed at each side of
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Date Recue/Date Received 2023-08-15
the restriction enzyme recognition site. In some examples, the use
of multiple (e.g. 2, 3, 4, 5, 6, 7 or 8 or more) probes per primary
restriction enzyme recognition site can be useful to minimize the
problem of obtaining false negative results from individual probes.
[00188] As used herein, the term "set of probes" refers to a
suite or a collection of probes that can hybridize to one or more
of the primary restriction enzyme recognition sites for a primary
restriction enzyme in a genome.
[00189] In some cases, a set of probes can be complementary in
sequence to the nucleic acid sequence adjacent to one or more of
the primary restriction enzyme recognition sites for a restriction
enzyme in genomic DNA. For example, the set of probes can be
complementary in sequence to the about 10 bp to 500 bp, about 10 bp
to 250 bp, about 20 bp to 250 bp, about 20 bp to 200 bp, about 25
bp to 200 bp, about 25 bp to 100 bp, about 30 bp to 100 bp, or
about 30 bp to 80 bp nucleotides that are adjacent to one or more
of the restriction enzyme recognition sites in genomic DNA. The set
of probes may be complementary in sequence to one (e.ge either)
side or both sides of the restriction enzyme recognition site.
Accordingly, the probes may be complementary in sequence to the
nucleic acid sequence adjacent to each side of one or more of the
primary restriction enzyme recognition sites in the genomic DNA.
Further, the set of probes can be complementary in sequence to the
nucleic acid sequence that is less than about 10 bp, about 20 bp.
about 30 bp, about 40 bp, about 50 bp, about 60 bp, about 70 bp,
about 80 bp, about 90 bp, about 100 bp, about 150 bp, about 200 bp,
about 250 bp, about 300 bp, about 400 bp, or about 500 bp from one
or more of the primary restriction enzyme recognition sites in
genomic DNA
[00190] In some cases, two or more probes can be designed to be
capable of hybridizing to the sequence adjacent to one or more of
the restriction enzyme recognition sites in genomic DNA. The probes
may overlap or partially overlap.
[001911 The probes, array of probes or set of probes can be
immobilized on a support. Supports (e.g. solid supports) can be
made of a variety of materials-such as glass, silica, plastic,
nylon or nitrocellulose. Supports are preferably rigid and have a
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planar surface. Supports can have from about 1 to 10,000,000
resolved loci. For example, a support can have about 10 to
10,000,000, about 10 to 5,000,000, about 100 to 5,000,000, about
100 to 4,000,000, about 1000 to 4,000,000, about 1000 to 3,000,000,
about 10,000 to 3,000,000, about 10,000 to 2,000,000, about 100,000
to 2,000,000, or about 100,000 to 1,000,000 resolved loci. The
density of resolved loci can be at least about 10, about 100, about
1000, about 10,000, about 100,000 or about 1,000,000 resolved loci
within a square centimeter. In some cases, each resolves loci can
be occupied by >95% of a single type of oligonucleotide. In other
cases, each resolved locus can be occupied by pooled mixtures of
probes or a set of probes. In further cases, some resolved loci are
occupied by pooled mixtures of probes or a set of probes, and other
resolved loci are occupied by >95% of a single type of
oligonucleotide.
[00192] In some cases, the number of probes for a given
nucleotide sequence on the array can be in large excess to the DNA
sample to be hybridized to such array. For example, the array can
have about 10, about 100, about 1000, about 10,000, about 100,000,
about 1,000,000, about 10,000,000, or about 100,000,000 times the
number of probes relative to the amount of DNA in the input sample.
[00193] In some cases, an array can have about 10, about 100,
about 1000, about 10,000, about 100,000, about 1,000,000, about
10,000,000, about 100,000,000, or about 1,000,000,000 probes.
[00194] Arrays of probes or sets of probes may be synthesized in
a step-by-step manner on a support or can be attached in
presynthesized form. One method of synthesis is VLSIPT" (as
described in U.S. Pat. No. 5,143,854 and EP 476,014), which entails
the use of light to direct the synthesis of oligonucleotide probes
in high-density, miniaturized arrays. Algorithms for design of
masks to reduce the nuMber of synthesis cycles are described in
U.S. Pat. No. 5,571,639 and U.S. Pat. No. 5,593,839. Arrays can
also be synthesized in a combinatorial fashion by delivering
monomers to cells of a support by mechanically constrained
flowpeths, as described in EP 624,059. Arrays can also be
synthesized by spotting reagents on to a. support using an ink jet
printer (see, for example, EP 728,520).
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[0D1951 In some embodiments, the present disclosure provides
methods for hybridizing the linked DNA segments onto an array. A
"substrate" or an "array" is an intentionally created collection of
nucleic acids which can be prepared either synthetically or
biosynthetically and screened for biological activity in a variety
of different formats (e.g., libraries of soluble molecules: and
libraries of oligonucleotides tethered to resin beads, silica
chips, or other solid supports). Additionally, the term "array"
Includes those libraries of nucleic acids which can be prepared by
spotting nucleic acids of essentially any length (e.g., from 1 to
about 1000 nucleotide monomers in length) onto a substrate.
(00196] Array technology and the various associated techniques
and applications are described generally in numerous textbooks and
documents. For example, these include Lemieux et al., 1998,
Molecular Breeding 4, 277-289; Schena and Davis, Parallel Analysis
with Biological Chips. in PR Methods Manual (ede. M. Innis, D.
Gelfand, J. Sninsky): Schena and Davis, 1999, Genes, Genomes and
Chips. In DNA Microarrays: A Practical Approach (ed. M. Schena),
Oxford University Press, Oxford, UK, 1999): The Chipping Forecast
(Nature Genetics special issue; January 1999 Supplement); Mark
Schena (Ed.), Alcroarray Biochip Technology, (Eaton Publishing
Company); Cortez, 2000, The Scientist 14[171:25: Gwynn and Page,
MIcroarray analysis: the next revolution in molecular biology,
Science, 1999 Aug. 6: and Eakins and Chu, 1999, Trends in
Biotechnology, 17, 217-218.
(00197] In general, any library may be arranged in an orderly
manner into an array, by spatially separating the members of the
library. Examples of suitable libraries for arraying include
nucleic acid libraries (including DNA, cDNA, oligonucleotide, etc.
libraries), peptide, polypeptide and protein libraries, as well as
libraries comprising any molecules, such as ligand libraries, among
others.
[00198] The library can be fixed or immobilized onto a solid
phase (e.g. a solid substrate), to limit diffusion and admixing of
the members. In some cases, libraries of DNA binding ligands may be
prepared. In particular, the libraries may be immobilized to a
substantially planar solid phase, including membranes and non-
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porous substrates such as plastic and glass. Furthermore, the
library can be arranged in such a way that indexing (i.e.,
reference or access to a particular member) is facilitated. In some
examples, the members of the library can be applied as spots in a
grid formation. Common assay systems may be adapted for this
purpose. For eyample, an array may be immobilized on the surface of
a microplate, either with multiple members in a well, or with a
single member in each well. Furthermore, the solid substrate may be
a membrane, such as a nitrocellulose or nylon membrane (for
example, membranes used in blotting experiments). Alternative
substrates include glass, or silica based substrates. Thus, the
library can be immobilized by any suitable method known in the art,
for example, by charge interactions, or by chemical coupling to the
walls or bottom of the wells, or the surface of the membrane. Other
means of arranging and fixing may be used, for example, pipetting,
drop-touch, piezoelectric means, ink-jet and bubblejet technology,
electrostatic application, etc. In the case of silicon-based chips,
photolithography may be utilized to arrange and fix the libraries
on the chip.
[001991 The library may be arranged by being "spotted" onto the
solid substrate; this may be done by hand or by making use of
robotics to deposit the members. In general, arrays may be
described as macroarrays or microarrays, the difference being the
size of the spots. Macroarrays can contain spot sizes of about 300
microns or larger and may be easily imaged by existing gel and blot
scanners. The spot sizes in microarrays can be less than 200
microns in diameter and these arrays usually contain thousands of
spots. Thus, microarrays may require specialized robotics and
imaging equipment, which may need to be custom made Instrumentation
is described generally in a review by Cortese, 2000, The Scientist
14[111:26.
[MOO] Techniques for producing immobilized libraries of DNA
molecules have been described in the art. Generally, most prior art
methods described how to synthesize single-stranded nucleic acid
molecule libraries, using for example masking techniques to build
up various permutations of sequences at the various discrete
positions on the solid substrate. U.S. Pat. No. 5,837,832 describes
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an improved method for producing DNA arrays immobilized to silicon
substrates based on very large scale integration technology. In
particular, U.S. Pat. No. 5,837,832 describes a strategy called
"tiling" to synthesize specific sets of probes at spatially-defined
locations on a substrate which may be used to produce the
immobilized DNA libraries of the present disclosure. U.S. Pat. No.
5,837,832 also provides references for earlier techniques that may
also be used. In other cases, arrays may also be built using photo
deposition chemistry.
[00201] Arrays of peptides (or peptidomimetics) may also be
synthesized on a surface in a manner that places each distinct
library member (e.g., unique peptide sequence) at a discrete,
predefined location in the array. The identity of each library
member is determined by its spatial location in the array. The
locations in the array where binding interactions between a
predetermined molecule (e.g., a target or probe) and reactive
library members occur is determined, thereby identifying the
sequences of the reactive library members on the basis of spatial
location. These methods are described in U.S. Pat. No. 5,143,854:
W090/15070 and W092/10092; Fodor et al. (1991) Science, 251: 767;
Dower and Fodor (1991) Ann. Rep. Med. Chem., 26: 271
[00202] To aid detection, labels can be used (as discussed
above)-such as any readily detectable reporter, for example, a
fluorescent, bioluminescent, phosphorescent, radioactive, etc.
reporter. Such reporters, their detection, coupling to
targets/probes, etc. are discussed elsewhere in this document.
Labelling of probes and targets is also disclosed in Shalon et al.,
1996, Genome Res 6(7):639-45.
[00203] Examples of some commercially available microarray
formats are set out in Table 1 below (see also Marshall and
Hodgson, 1998, Mature Biotechnology, 16(1), 27-31).
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TABLE 1
Examples of currently available hybridization microarray formats
Company Product Name Arraying Method Hybridization Step Readout
Affymetrix, GeneChip In Situ (on-chip) 10,000-260,000 oligo
Fluorescence
Inc., Santa photolithographic features probed with
Clara, synthesis of ¨20-25-mer labeled 30-40
California oligos onto silicon nucleotide fragments of
wafers, which are diced sample cDNA or
into 1.25 cm2 or 5.25 cm2 antisense RNA
chips
Brax, Short synthetic oligo, 1000 oligos
on a Mass spectrometry
Cambridge, synthesized off-chip "universal chip" probed
UK with tagged nucleic acid
Gene Logic, READS 1191
Inc., Columbia,
Maryland
Genometrix Universal
Inc., The ArraysTm
Woodlands,
Texas
GENSET,
Paris, France
Hyseq Inc., HyChip TN 500-2000 nt DNA 64 sample cDNA spots
Radioisotope
Sunnyvale, samples printed onto 0.6 probed with 8,000 7-
California cm2 (HyGnostics) or ¨18 mer oligos (HyGnostics)
cm2 (Gene Discovery) of <=55,000 sample
membranes cDNA spots probed with
300 7-mer oligo (Gene
Discovery
Fabricated 5-mer oligos Universal 1024 oligo
Fluorescence
printed as 1.15 cm2 spots probed 10kb
arrays onto glass sample cDNAs, labeled
(HyChip) 5-mer oligo, and ligase
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TABLE 1-continued
Examples of currently available hybridization microarray formats
Company Product Name Arraying Method Hybridization Step
Readout
Incyte GEM Piezoelectric printing for <=1000
(eventually Fluorescence
Pharmaceuticals, spotting PCR fragments 10,000) oligo/PCR
and
Inc., Palo Alto, and on-chip synthesis of fragment spots
probed radioisotope
California oligos with labeled RNA
Molecular Dynamics, Storm 500-5000 nt cDNAs printed -10,000 cDNA spots
Fluorescence
Inc., Sunnyvale, FluorImager by pen onto -10 cm2 on
probed with 200-400
California glass slide nt labeled sample
cDNAs
Nanogen, San Diego, Semiconductor Prefabricated -20-mer 25, 64,
400 (and Fluorescence
California Microchip oligos, captured onto eventually 10,000)
electroactive spots on oligo spots polarized
silicon wafers, which are to enhance
diced into <=1 cm2 chips hybridization to 200-
400 nt labeled sample
cDNAs
Protogene On-chip synthesis of 40- <=8,000
oligo spots Fluorescence
Laboratories, Palo 50-mer oligos onto 9 cm2 probed with 200-400
Alto, California glass chip via printing to a nt labeled
sample
surface-tension array nucleic acids
Sequenom, M2ssArray Off-set printing of array; 250
locations per Mass
Hamburg, Germany, SpectroChip around 20-25-mer oligos
SpectroChip spectrometry
and San Diego, interrogated by laser
California desorbtion and mass
spectrometry
Synteni, Inc., UniGEMTm 500-5,000 nt cDNAs <=10,000 cDNA spots
Fluorescence
Fremont, California printed by tip onto -4 cm2 probed with 200-
400
glass chip nt labeled sample
cDNAs
Nimblegen Systems Homo sapiens 38,000 transcripts with 5 5-micron
Inc., Madison Whole- probes per gene 17.4 mm scanning
Genome x 13 mm platform
60mer
Microarray
The German Cancer Prototypic PNA macrochip Around 1,000 spots on
Fluorescence/
Institute, Heidelberg, with on-chip synthesis of a 8 x 12
cm chip mass
Germany probes using f-moc or t-
spectrometry
moc chemistry
[00204] in order to generate data from array-based assays a
signal can detected to signify the presence of or absence of
hybridization between a probe and a nucleotide sequence. Further,
direct and indirect labeling techniques can also be utilized. For
example, direct labeling incorporates fluorescent dyes directly
into the nucleotide sequences that hybridize to the array
associated probes (e.g., dyes are Incorporated into nucleotide
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Date Recue/Date Received 2023-08-15
sequence by eneymatic synthesis in the presence of labeled
nucleotides or SCR primers). Direct labeling schemes can yield
strong hybridization signals, for example by using families of
fluorescent dyes with similar chemical structures and
characteristics, and can be simple to implement. In cases
comprising direct labeling of nucleic acids, cyanine or alexa
analogs can be utilized in multiple-fluor comparative array
analyses. In other embodiments, indirect labeling schemes can be
utilized to incorporate epitopes into the nucleic acids either
prior to ox after hybridization to the microarray probes. One or
more staining procedures and reagents can be used to label the
hybridized complex (e.g., a fluorescent molecule that binds to the
epitopes, thereby providing a fluorescent signal by virtue of the
conjugation of dye molecule to the epitope of the hybridized
species).
[00205] In various embodiments, suitable sequencing methods
described herein or otherwise known in the art will be used to
obtain sequence information from nucleic acid molecules within a
sample. sequencing can be accomplished through classic Sanger
sequencing methods which are well known in the art. Sequence can
also be accomplished using high-throughput systems some of which
allow detection of a sequenced nucleotide immediately after or upon
its incorporation into a growing strand, i.e., detection of
sequence in real time or substantially real time. In some cases,
high throughput sequencing generates at least 1,000, at least
5,000, at least 10,000, at least 20,000, at least 30,000, at least
40,000, at least 50,000, at least 100,000 or at least 500,000
sequence reads per hour; where the sequencing reads can be at least
about 50, about 60, about 70, about 80, about 90, about 100, about
120, about 150, about 180, about 210, about 240, about 270, about
300, about 350, about 400, about 450, about 500, about 600, about
700, about 800, about 900, or about 1000 bases per read.
[00206] In some embodiments, high-throughput sequencing involves
the use of technology available by Illumina's Genome Analyzer IN,
MiSeq personal sequencer, or HiSeq systems, such as those using
HiSeq 2500, HiSeq 1500, HiSeq 2000, or Hiseq 1000 machines. These
machines use reversible terminator-based sequencing by synthesis
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Date Recue/Date Received 2023-08-15
chemistry. These machine can do 200 billion DNA reads or more in
eight days. Smaller systems may be utilized for runs within 3, 2, 1
days or less time.
[00207] In some embodiments, high-throughput sequencing involves
the use of technology available by ABI Solid System. This genetic
analysis platform that enables massively parallel sequencing of
clonally-amplified DNA fragments linked to beads. The sequencing
methodology is based on sequential ligation with dye-labeled
oligonucleotides.
[00208] The next generation sequencing can comprise ion
semiconductor sequencing (e.g., using technology from Life
Technologies (Ion Torrent)). Ion semiconductor sequencing can take
advantage of the fact that when a nucleotide is incorporated into a
strand of DNA, an ion can be released. To perform ion semiconductor
sequencing, a high density array of micromachined wells can be
formed. Each well can hold a single DNA template. Beneath the well
can be an ion sensitive layer, and beneath the ion sensitive layer
can be an ion sensor. When a nucleotide is added to a DNA, H+ can
be released, which can be measured as a change in pH. The H+ ion
can be converted to voltage and recorded by the semiconductor
sensor. An array chip can be sequentially flooded with one
nucleotide after another. No scanning, light, or cameras can be
required. In some cases, an IONPROTOW Sequencer is used to
sequence nucleic acid. In some cases, an IONPGM' Sequencer is used.
The Ion Torrent Personal Genome Machine (PGM). The PGM can do 10
million reads in two hours.
[00209] In some embodiments, high-throughput sequencing involves
the use of technology available by Helicos BioSciences Corporation
(Cambridge, Massachusetts) such as the Single Molecule Sequencing
by Synthesis (SMSS) meLhod. SMSS is unique because it allows for
sequencing the entire human genome in up to 24 hours. Finally,
SMSS is described in part in US Publication Application Nos.
20060024711; 20060024678; 20060012793; 20060012784; and
20050100932.
[00210] In some embodiments, high-throughput sequencing involves
the use of technology available by 454 Lifesciences, Inc.
(Branford, Connecticut) such as the PicoTiterPlate device which
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includes a fiber optic plate that transmits chemiluminescent signal
generated by the sequencing reaction to be recorded by a CCD camera
in the instrument. This use of fiber optics allows for the
detection of a minimum of 20 million base pairs in 4.5 hours.
[00211] Methods for using bead amplification followed by fiber
optics detection are described in Marguiles, M., et al. "Genome
sequencing in microfabricated high-density pricolitre reactors",
Nature, doi:10.1038/nature03959; and well as in US Publication
Application Nos. 20020012930; 20030068629; 20030100102; 20030148344
; 20040248161; 20050079510, 20050124022; and 20060078909.
[00212] In some embodiments, high-throughput sequencing is
performed using Clonal Single Molecule Array (Solexa, Inc.) or
sequencing-by-synthesis (SpS) utilizing reversible terminator
chemistry. These technologies are described in part in US Patent
Nos. 6,969,488; 6,897,023; 6,833,246; 6,787,308; and US Publication
Application Nos. 20040106110; 20030064398; 20030022207; and
Constans, A., The Scientist 2003, 17(13):36.
[002131 The next generation sequencing technique can comprises
real-time (SMRTm) technology by Pacific Biosciences. In SMRT, each
of four DNA bases can be attached to one of four different
fluorescent dyes. These dyes can be phospho linked. A single DNA
polymerase can be immobilized with a single molecule of template
single stranded DNA at the bottom of a zero-mode waveguide (ZMW). A
ZMW can be a confinement structure which enables observation of
incorporation of a single nucleotide by DNA polymerase against the
background of fluorescent nucleotides that can rapidly diffuse in
an out of the ZMW (in microseconds). It can take several
milliseconds to incorporate a nucleotide into a growing strand.
During this time, the fluorescent label can be excited and produce
a fluorescent signal, and the fluorescent, Lag can be cleaved off.
The ZMW can be illuminated from below. Attenuated light from an
excitation beam can penetrate the lower 20-30 nm of each ZMW. A
microscope with a detection limit of 20 zepto liters (10" liters)
can be created. The tiny detection volume can provide 1000-fold
improvement in the reduction of background noise. Detection of the
corresponding fluorescence of the dye can indicate which base was
incorporated. The process can be repeated.
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Date Recue/Date Received 2023-08-15
[002141 In some cases, the next generation sequencing is
nanopore sequencing (See, e.g., Soni GV and Meller A. (2007) Clin
Chem 53: 1996-2001). A nanopore can be a small hole, of the order
of about one nanometer in diameter. Immersion of a nanopore in a
conducting fluid and application of a potential across it can
result in a slight electrical current due to conduction of ions
through the nanopore. The amount of current which flows can be
sensitive to the size of the nanopore. As a DNA molecule passes
through a nanopore, each nucleotide on the DNA molecule can
obstruct the nanopore to a different degree. Thus, the change in
the current passing through the nanopore as the DNA molecule passes
through the nanopore can represent a reading of the DNA sequence.
The nanopore sequencing technology can be from Oxford Nanopore
Technologies; e.g., a GridlON system. A single nanopore can be
inserted in a polymer membrane across the top of a microwell. Each
microwell can have an electrode for individual sensing. The
microwells can be fabricated into an array chip, with 100,000 or
more microwells (e.g., more than 200,000, 300,000, 400,000,
500,000, 600,000, 700,000, 800,000, 900,000, or 1,000,000) per
chip. An instrument (or node) can be used to analyze the chip. Data
can be analyzed in real-time. One or more instruments can be
operated at a time. The nanopore can be a protein nanopore, e.g.,
the protein alpha-hemolysin, a heptameric protein pore. The
nanopore can be a solid-state nanopore made, e.g., a nanometer
sized hole formed in a synthetic membrane (e.g., SiNõ or SiO2). The
nanopore can be a hybrid pore (e.g., an integration of a protein
pore into a solid-state membrane). The nanopore can be a nanopore
with an integrated sensors (e.g., tunneling electrode detectors,
capacitive detectors, or graphene based nano-gap or edge state
detectors (see e.g., Garaj eL al. (2010) Nature vol. 67, doi:
10.1038/nature09379)). A nanopore can be functionalized for
analyzing a specific type of molecule (e.g., DNA, RNA, or protein).
Nanopore sequencing can comprise "strand sequencing" in which
intact DNA polymers can be passed through a protein nanopore with
sequencing in real time as the DNA translocates the pore. An enzyme
can separate strands of a double stranded DNA and feed a strand
through a nanopore. The DNA can have a hairpin at one end, and the
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Date Recue/Date Received 2023-08-15
system can read both strands. In some cases, nanopore sequencing is
"exonuclease sequencing" in which individual nucleotides can be
cleaved from a DNA strand by a processive exonuclease, and the
nucleotides can be passed through a protein nanopore. The
nucleotides can transiently bind to a molecule in the pore (e.g.,
cyclodextran). A characteristic disruption in current can be used
to identify bases.
[002151 Nanopore sequencing technology from GENIA can be used.
An engineered protein pore can be embedded in a lipid bilayer
membrane. "Active Control" technology can be used to enable
efficient nanopore-membrane assembly and control of DNA movement
through the channel. In some cases, the nanopore sequencing
technology is from NABsys. Genomic DNA can be fragmented into
strands of average length of about 100 kb. The 100 kb fragments can
be made single stranded and subsequently hybridized with a 6-mer
probe. The genomic fragments with probes can be driven through a
nanopore, which can create a current-versus- time tracing. The
current tracing can provide the positions of the probes on each
genomic fragment. The genomic fragments can be lined up to create a
probe map for the genome. The process can be done in parallel for a
library of probes. A genome-length probe map for each probe can be
generated. Errors can be fixed with a process termed "moving window
Sequencing By Hybridization (mwSBH)." In some cases, the nanopore
sequencing technology is from IDM/Roche. An electron beam can be
used to make a nanopore sized opening in a microchip. An electrical
field can be used to pull or thread DNA through the nanopore. A DNA
transistor device in the nanopore can comprise alternating
nanometer sized layers of metal and dielectric. Discrete charges in
the DNA backbone can get trapped by electrical fields inside the
DNA nanopore. Turning off and on gaLe vollages can allow the DNA
sequence to be read.
[00216] The next generation sequencing can comprise DNA nanoball
sequencing (as performed, e.g., by Complete Genomics; see e.g.,
Drmanac et al. (2010) Science 327: 78-81). DNA can be isolated,
fragmented, and size selected. For example, DNA can be fragmented
(e.g., by sonication) to a mean length of about 500 bp. Adaptors
(hdl) can be attached to the ends of the fragments. The adaptors
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can be used to hybridize to anchors for sequencing reactions. DNA
with adaptors bound to each end can be PCR amplified. The adaptor
sequences can be modified so that complementary single strand ends
bind to each other forming circular DNA. The DNA can be methylated
to protect it from cleavage by a type IIS restriction enzyme used
in a subsequent step. An adaptor (e.g., the right adaptor) can have
a restriction recognition site, and the restriction recognition
site can remain non-methylated. The non-methylated restriction
recognition site in the adaptor can be recognized by a restriction
enzyme (e.g., Acul), and the DNA can be cleaved by Acul 13 bp to
the right of the right adaptor to form linear double stranded DNA.
A second round of right and left adaptors (Ad2) can be ligated onto
either end of the linear DNA, and all DNA with both adapters bound
can be PCR amplified (e.g., by PCR). Ad2 sequences can be modified
to allow them to bind each other and form circular DNA. The DNA can
be methylated, but a restriction enzyme recognition site can remain
non-methylated on the left Adl adapter. A restriction enzyme (e.g.,
Acul) can be applied, and the DNA can be cleaved 13 bp to the left
of the Adl to form a linear DNA fragment. A third round of right
and left adaptor (Ad3) can be ligated to the right and left flank
of the linear DNA, and the resulting fragment can be PCR amplified.
The adaptors can be modified so that they can bind to each other
and form circular DNA. A type III restriction enzyme (e.g., EcoP15)
can be added; EcoP15 can cleave the DNA 26 bp to the left of Ad3
and 26 bp to the right of Ad2. This cleavage can remove a large
segment of DNA and linearize the DNA once again. A fourth round of
right and left adaptors (Ad4) can be ligated to the DNA, the DNA
can be amplified (e.g., by PCR), and modified so that they bind
each other and form the completed circular DNA template.
[00217] Rolling circle replicaLion (e.g., using Phi 29 DNA
polymerase) can be used to amplify small fragments of DNA. The four
adaptor sequences can contain palindromic sequences that can
hybridize and a single strand can fold onto itself to form a DNA
nanoball (Mi) which can be approximately 200-300 nanometers in
diameter on average. A DNA nanoball can be attached (e.g., by
adsorption) to a microarray (sequencing flowcell). The flaw cell
can be a silicon wafer coated with silicon dioxide, titanium and
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Date Recue/Date Received 2023-08-15
hexamehtyldisilazane (HMDS) and a photoresist material. Sequencing
can be performed by unchained sequencing by ligating fluorescent
probes to the DNA. The color of the fluorescence of an interrogated
position can be visualized by a high resolution camera. The
identity of nucleotide sequences between adaptor sequences can be
determined.
[00218] In some embodiments, high-throughput sequencing can take
place using AnyDot.chips (Genovoxx, Germany). In particular, the
AnyDot.chips allow for 10x - 50x enhancement of nucleotide
fluorescence signal detection. AnyDot.chips and methods for using
them are described in part in International Publication Application
Nos. WO 02088382, WO 03020968, WO 03031947, WO 2005044836, PCT/EP
05/05657, PCT/EP 05/05655; and German Patent Application Nos. DE
101 49 786, DE 102 14 395, DE 103 56 837, DE 10 2004 009 704, DE 10
2004 025 696, DE 10 2004 025 746, DE 10 2004 025 694, DE 10 2004
025 695, DE 10 2004 025 744, DE 10 2004 025 745, and DE 10 2005 012
301.
[00219] Other high-throughput sequencing systems include those
disclosed in Venter, J., et al. Science 16 February 2001; Adams, M.
et a/. Science 24 March 2000; and M. J. Levene, et al. Science
299:682-686, January 2003; as well as US Publication Application
No. 20030044781 and 2006/0078937. Overall such system involve
sequencing a target nucleic acid molecule having a plurality of
bases by the temporal addition of bases via a polymerization
reaction that is measured on a molecule of nucleic acid, i.e. the
activity of a nucleic acid polymerizing enzyme on the template
nucleic acid molecule to be sequenced is followed in real time.
Sequence can then be deduced by identifying which base is being
incorporated into the growing complementary strand of the target
nucleic acid by Lhe caLalytic acliviLy of Lhe nucleic acid
polymerizing enzyme at each step in the sequence of base additions.
A polymerase on the target nucleic acid molecule complex is
provided in a position suitable to move along the target nucleic
acid molecule and extend the oligonucleotide primer at an active
site. A plurality of labeled types of nucleotide analogs are
provided proximate to the active site, with each distinguishable
type of nucleotide analog being complementary to a different
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nucleotide in the target nucleic acid sequence. The growing nucleic
acid strand is extended by using the pclymerase to add a nucleotide
analog to the nucleic acid strand at the active site, where the
nucleotide analog being added is complementary to the nucleotide of
the target nucleic acid at the active site. The nucleotide analog
added to the oligonucleotide primer as a result of the polymerizing
step is identified. The steps of providing labeled nucleotide
analogs, polymerizing the growing nucleic acid strand, and
identifying the added nucleotide analog are repeated so that the
nucleic acid strand is further extended and the sequence of the
target nucleic acid is determined.
[00220] In particular embodiments, the present disclosure
further provides kits comprising one or more components of the
disclosure. The kits can be used for any application apparent to
those of skill in the art, including those described above. The
kits can comprise, for example, a plurality of association
molecules, a fixative agent, a restriction endonuclease, a ligase,
and/or a combination thereof. In some cases, the association
molecules can be proteins including, for example, histones. In some
cases, the fixative agent can be formaldehyde or any other DNA
crosslinking agent.
[00221] In some cases, the kit can further comprise a plurality
of beads. The beads can be paramagnetic and/or are coated with a
capturing agent. For example, the beads can be coated with
streptavidin and/or an antibody.
[00222] In some cases, the kit can comprise adaptor
oligonucleotides and/or sequencing primers. Further, the kit can
comprise a device capable of amplifying the read-pairs using the
adaptor oligonucleotides and/or sequencing primers.
[00223] In some cases, the kit can also comprise other reagents
including but not limited to lysis buffers, ligation reagents (e.g.
dNTPs, polymerase, polynucleotide kinase, and/ or ligase buffer,
etc.), and PCR reagents (e.g. dNTPs, polymerase, and/or ACR buffer,
etc.),
[00224] The kit can also include instructions for using the
components of the kit and/or for generating the read-pairs.
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[00225] The computer system 500 illustrated in FIG. 8 may be
understood as a logical apparatus that can read instructions from
media 511 and/or a network port 505, which can optionally be
connected to server 509 having fixed media 512. The system, such as
shown in FIG. 8 can include a CPU 501, disk drives 503, optional
input devices such as keyboard 515 and/or mouse 516 and optional
monitor 507. Data communication can be achieved through the
indicated communication medium to a server at a local or a remote
location. The communication medium can include any means of
transmitting and/or receiving data. For example, the communication
medium can be a network connection, a wireless connection or an
internet connection. Such a connection can provide for
communication over the World Wide Web. It is envisioned that data
relating to the present disclosure can be transmitted over such
networks or connections for reception and/or review by a party 522
as illustrated in FIG. 8.
[00226] FIG. 9 is a block diagram illustrating a first example
architecture of a computer system 100 that can be used in
connection with example embodiments of the present disclosure. As
depicted in FIG. 9, the example computer system can include a
processor 102 for processing instructions. Non-limiting examples
of processors include: Intel Xeonn't processor, AMD Opteron"
processor, Samsung 32-bit RISC ARM 1176JZ(F)-S v1.0" processor, ARM
Cortex-A8 Samsung S5PC100" processor, ARM Cortex-A8 Apple A4"
processor, Marvell PKA 930" processor, or a functionally-equivalent
processor. Multiple threads of execution can be used for parallel
processing. In some embodiments, multiple processors or processors
with multiple cores can also be used, whether in a single computer
system, in a cluster, or distributed across systems over a network
comprising a plurality of computers, cell phones, and/or personal
data assistant devices.
[00227] As illustrated in FIG. 9, a high speed cache 104 can be
connected to, or incorporated in, the processor 102 to provide a
high speed memory for instructions or data that have been recently,
or are frequently, used by processor 102. The processor 102 is
connected to a north bridge 106 by a processor bus 108. The north
bridge 106 is connected to random access memory (RAM) 110 by a
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memory bus 112 and manages access to the RAM 110 by the processor
102. The north bridge 106 is also connected to a south bridge 114
by a chipset bus 116. The south bridge 114 is, in turn, connected
to a peripheral bus 118. The peripheral bus can be, for example,
PCI, PCI Express, or other peripheral bus. The north bridge
and south bridge are often referred to as a processor chipset and
manage data transfer between the processor, RAM, and peripheral
components on the peripheral bus 118. /n some alternative
architectures, the functionality of the north bridge can be
incorporated into the processor instead of using a separate north
bridge chip.
[00228] In some embodiments, system 100 can include an
accelerator card 122 attached to the peripheral bus 118. The
accelerator can include field programmable gate arrays (FPGAs) or
other hardware for accelerating certain processing. For example, an
accelerator can be used for adaptive data restructuring or to
evaluate algebraic expressions used in extended set processing.
[00229] Software and data are stored in external storage 124 and
can be loaded into RAM 110 and/or cache 104 for use by the
processor. The system 100 includes an operating system for managing
system resources; non-limiting examples of operating systems
include: Linux, Windowsw-, MACOSm, BlackBerry OS, i051/4, and other
functionally-equivalent operating systems, as well as application
software running on top of the operating system for managing data
storage and optimization in accordance with example embodiments of
the present disclosure.
[00230] In this example, system 100 also includes network
interface cards (NICs) 120 and 121 connected to the peripheral bus
for providing network interfaces to external storage, such as
Network Attached Storage (NAS) and other computer systems that can
be used for distributed parallel processing.
[00231] FIG. 10 is a diagram showing a network 200 with a
plurality of computer systems 202a, and 202b, a plurality of cell
phones and personal data assistants 202c, and Network Attached
Storage (NAS) 204a, and 204b. In example embodiments, systems 202a,
202b, and 202c can manage data storage and optimize data access for
data stored in Network Attached Storage (NAS) 204a and 204b. A
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Date Recue/Date Received 2023-08-15
mathematical model can be used for the data and be evaluated using
distributed parallel processing across computer systems 202a, and
202b, and cell phone and personal data assistant systems 202c.
Computer systems 202a, and 202b, and cell phone and personal data
assistant systems 202c can also provide parallel processing for
adaptive data restructuring of the data stored in Network Attached
Storage (NAS) 204a and 204b. FIG. 10 illustrates an example only,
and a wide variety of other computer architectures and systems can
be used in conjunction with the various embodiments of the present
disclosure. For example, a blade server can be used to provide
parallel processing. Processor blades can be connected through a
back plane to provide parallel processing. Storage can also be
connected to the back plane or as Network Attached Storage (NAS)
through a separate network interface.
[00232] In some example embodiments, processors can maintain
separate memory spaces and transmit data through network
interfaces, back plane or other connectors for parallel processing
by other processors. In other embodiments, some or all of the
processors can use a shared virtual address memory space.
[00233] FIG. 11 is a block diagram of a multiprocessor computer
system 300 using a shared virtual address memory space in
accordance with an example embodiment. The system includes a
plurality of processors 302a-f that can access a shared memory
subsystem 304. The system incorporates a plurality of programmable
hardware memory algorithm processors (MAPs) 306a-f in the memory
subsystem 304. Each MAP 306a-f can comprise a memory 308a-f and one
or more field programmable gate arrays (FPGAs) 310a-f. The MAP
provides a configurable functional unit and particular algorithms
or portions of algorithms can be provided to the FPGAs 310a-f for
processing in close coordination with a respective processor. For
example, the MAPS can be used to evaluate algebraic expressions
regarding the data model and to perform adaptive data restructuring
in example embodiments. In this example, each MAP is globally
accessible by all of the processors for these purposes. In one
configuration, each MAP can use Direct Memory Access (DMA) to
access an associated memory 308a-f, allowing it to execute tasks
independently of, and asynchronously from, the respective
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microprocessor 302a-f. In this configuration, a MAP can feed
results directly to another MAP for pipelining and parallel
execution of algorithms.
[00234] The above computer architectures and systems are
examples only, and a wide variety of other computer, cell phone,
and personal data assistant architectures and systems can be used
in connection with example embodiments, including systems using any
combination of general processors, co-processors, FPGAs and other
programmable logic devices, system on chips (SOCs), application
specific integrated circuits (ASICs), and other processing and
logic elements. In some embodiments, all or part of the computer
system can be implemented in software or hardware. Any variety of
data storage media can be used in connection with example
embodiments, including random access memory, hard drives, flash
memory, tape drives, disk arrays, Network Attached Storage (NAS)
and other local or distributed data storage devices and systems.
[00235] In example embodiments, the computer system can be
implemented using software modules executing on any of the above or
other computer architectures and systems. In other embodiments, the
functions of the system can be implemented partially or completely
in firmware, programmable logic devices such as field programmable
gate arrays (FPGAs) as referenced in FIG. 11, system on chips
(SOCs), application specific integrated circuits (ASICs), or other
processing and logic elements. For example, the Set Processor and
Optimizer can be implemented with hardware acceleration through the
use of a hardware accelerator card, such as accelerator card 122
illustrated in FIG. 9.
[00236] The following examples are intended to illustrate but
not limit the disclosure. While they are typical of those that
might be used, other procedures known to those skilled in the art
may alternatively be used.
EXAMPLES
[00237] Example 1. Methods to generate chromatin in vitro
[00238] Two approaches to reconstitute chromatin are of
particular attention: one approach is to use ATP-independent random
deposition of histones onto DNA, while the other approach uses ATP-
dependent assembly of periodic nucleosomes. The disclosure allows
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the use of either approach with one or more methods disclosed
herein. Examples of both approaches to generate chromatin can be
found in Lusser et al. ("Strategies for the reconstitution of
chromatin," Nature Methods (2004), 1(l):19-26).
[00239] Example 2. Genome Assembly Using HI-C Based Techniques
[00240] A genome from a human subject was fragmented into
pseudo-contigs having a size of 500 kb. Using a Hi-C based method,
a plurality of read pairs were generated by probing the physical
layout of chromosomes within living cells. Any number of Hi-C
based methods can be used to generate read pairs, including the
method presented in Lieberman-Aiden et a/. ("Comprehensive mapping
of long range interactions reveals folding principles of the human
genome," Science (2009), 326(5950):289-2931
Read pairs
were mapped to all pseudo-contigs and those pairs that mapped to
two separate pseudo-contigs, were used to construct an adjacency
matrix based upon the mapping data. At least about 50%, about 60%,
about 70%, about 80%, about 90%, about 95% or about 99% of the read
pairs were weighted by taking a function of the read's distance to
the edge of the pseudo-contig so as to mathematically incorporate
the empirically known higher probability of shorter contacts than
longer contacts. Then, for each pseudo-contig, the adjacency matrix
was analyzed to determine a path through the pseudo-contigs by
finding the single best neighbor pseudo-contig, which was
determined by having the highest sum-of-weights. By performing
these methods, it was found that > 97% of all pseudo-contigs
identified their correct neighbor. Additional experiments can be
performed to test the impact of shorter contigs and alternate
weighting and path-finding schemes.
[00241] Alternatively, genome assembly using Hi-C data can
include computational methods that exploit the signal of genomic
proximity in Hi-C data sets for ultra-long scaffolding of de nova
genome assemblies. Examples of such computational methods that can
used with the methods disclosed herein, include the ligating
adjacent chromatin method by Burton et al. (Nature Biotechnology
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Date Recue/Date Received 2023-08-15
31:1119-1125 (2013)); and a DNA triangulation method by Kaplan et
al. (Nature Biotechnology 31:1143-47 12013)).
Further, it should be understood that these computational methods
can be used in combination, including with the other genome
assembly methods presented herein.
[00242] For example, a ligating adjacent chromatin method based
on Burton et al. comprising the steps of (a) clustering contigs to
chromosome groups, (b) ordering the contigs within one or more
chromosome group, and then (c) assigning relative orientations to
individual contigs, can be used with the methods disclosed herein.
For step (a), contigs are placed into groups using hierarchical
clustering. A graph is built, with each node initially repre-
senting one contig, and each edge between nodes having a weight
equal to the number of Hi-C read-pairs linking the two contigs. The
contigs are merged together using hierarchical agglomerative
clustering with an average-linkage metric, which is applied until
the number of groups are reduced to the expected number of distinct
chromosomes (counting only groups with more than one contig).
Repetitive contigs (contigs whose average link density with other
contigs, normalized by number of restriction fragment sites, is
greater than two times the average link density) and contigs with
too few restriction fragment sites are not clustered. However,
after clustering, each of these contigs is assigned to a group if
its average link density with that group is greater than four times
its average link densities with any other group. For step (b), a
graph is built as in the clustering step, but with the edge weights
between nodes equal to the inverse of the number of Hi-C links
between the contigs, normalized by the number of restriction
fragment sites per contig. Short contigs are excluded from this
graph. A minimum spanning tree is calculated for this graph. The
longest path in this tree, the "trunk", is found. The spanning tree
is then modified so as to lengthen the trunk by adding to it
contigs adjacent to the trunk, in ways that keep the total edge
weight heuristically low. After a lengthened trunk is found for
each group, it is converted into a full ordering as follows. The
trunk is removed from the spanning tree, leaving a set of
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"branches" containing all contigs not in the trunk. These branches
are reinserted into the trunk, the longest branches first, with the
insertion sites chosen so as to maximize the number of links
between adjacent contigs in the ordering. Short fragments are not
reinserted; as a result, many small contigs that were clustered are
left out of the final assembly. For step (c), the orientation of
each contig within its ordering is determined by taking into
account the exact position of the Hi-C link alignments on each
contig. It is assumed that the likelihood of a Hi-C link connecting
two reads at a genomic distance of x is roughly l/x for x -100
Kb. A weighted, directed, acyclic graph (WDAG) is built
representing all possible ways to orient the contigs in the given
order. Each edge in the WDAG corresponds to a pair of adjacent
contigs in one of their four possible combined orientations, and
the edge weight is set to the log-likelihood of observing the set
of Hi-C link distances between the two contigs, assuming they are
immediately adjacent with the given orientation. For each contig, a
quality score for its orientation is calculated as follows. The
log-likelihood of the observed set of Hi-C links between this
contig, in its current orientation, and its neighbors, is found.
Then the contig is flipped and the log-likelihood is calculated
again. The first log-likelihood is guaranteed to be higher because
of how the orientations are calculated. The difference between the
log-likelihoods is taken as a quality score.
[00243] An alternative DNA triangulation method similar to
Kaplan et al. can also be used in the methods disclosed herein to
assemble a genome from contigs and read pairs. DNA triangulation
is based upon the use of high-throughput in vivo genome-wide
chromatin interaction data to infer genomic location. For the DNA
triangulation method, the CTR pattern is first quantified by
partitioning a genome into 100-kb bins, each representing a large
virtual contig, and calculating for each placed contig its average
interaction frequency with each chromosome. To evaluate
localization over long ranges, interaction data of a contig with
its flanking 1 mb on each side is omitted. The average interaction
frequency strongly separates inter- from intrachromosomal
interactions, and is highly predictive of which chromosome a contig
Date Recue/Date Received 2023-08-15
belongs to. Next, a simple multiclass model, a naive Bayes
classifier, is trained to predict the chromosome of each contig
based on its average interaction frequency with each chromosome.
The assembled portion of the genome is used to fit a probabilistic
single-parameter exponential decay model describing the
relationship between Hi-C interaction frequency and genomic
distance (the DDD pattern). In each turn, a contig is removed from
the chromosome, along with a flanking region of 1 Mb on each side.
It is then estimated the most likely position for each contig based
upon the interaction profile and decay model. The prediction error
is quantified as the absolute value of the distance between the
predicted position and the actual position.
[00244] By combining the DNA triangulation method with long-
insert libraries the predictability for each contig can be further
improved. By knowing the chromosomal assignment and approximate
location of each contig could significantly reduce the
computational complexity of long-insert scaffolding, as each contig
need only be paired with contiqs in its vicinity; thereby resolving
ambiguous contig joining, and reduce assembly errors where contigs
which are located at distant regions of a chromosome or on
different chromosomes, are incorrectly joined.
[00245] Example 3. Methods for Haplotype Phasing
[00246] Because the read pairs generated by the methods
disclosed herein are generally derived from intra-chromosomal
contacts, any read pairs that contain sites of heterozygosity will
also carry information about their phasing. Using this
information, reliable phasing over short, intermediate and even
Long (megabase) distances can be performed rapidly and accurately.
Experiments designed to phase data from one of the 1000 genomes
trios (a set of mother/father/offspring genomes) have reliably
inferred phasing. Additionally, haplotype reconstruction using
proximity-ligation similar to Selvaraj et al. (Nature Biotechnology
31:1111-1118 (2013)) can also be used with haplotype phasing
methods disclosed herein.
[00247] For example, a haplotype reconstruction using proximity-
ligation based method can also be used in the methods disclosed
herein in phasing a genome. A haplotype reconstruction using
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proximity-ligation based method combines a proximity-ligation and
DNA sequencing with a probabilistic algorithm for haplotype
assembly. First, proximity-ligation sequencing is performed using a
chromosome capture protocol, such as Hi-C protocol. These methods
can capture DNA fragments from two distant gehomic loci that looped
together in three-dimensional space. After shotgun DNA-sequencing
of the resulting DNA library, paired-end sequencing reads have
'insert sizes' that range from several hundred base pairs to tens
of millions of base pairs. Thus, short DNA fragments generated in a
Hi-C experiment can yield small haplotype blocks, long fragments
ultimately can link these small blocks together. With enough
sequencing coverage, this approach has the potential to link
variants in discontinuous blocks and assemble every such block into
a single haplotype. This data is then combined with a proba-
bilistic algorithm for haplotype assembly. The probabilistic
algorithm utilizes a graph in which nodes correspond to
heterozygous variants and edges correspond to overlapping sequence
fragments that may link the variants. This graph might contain
spurious edges resulting from sequencing errors or trans
interactions. A max-cut algorithm is then used to predict par-
simonious solutions that are maximally consistent with the
haplotype information provided by the set of input sequencing
reads. Because proximity ligation generates larger graphs than
conventional genome sequencing or mate-pair sequencing, computing
time and number of iterations are modified so that the haplotypes
can be predicted with reasonable speed and high accuracy. The
resulting data can then be used to guide local phasing using Beagle
software and sequencing data from the genome project to generate
chromosome-spanning haplotypes with high resolution and accuracy.
[00248] Example 4. Methods for Meta-genomic assembly
[00249] microbes are collected from an environment and fixed
with a fixative agent, such as formaldehyde, in order to form
cross-links within the microbial cells. A plurality of contigs
from the microbes is generated by using high-throughput sequencing.
A plurality of read pairs are generated by using Hi-C based
techniques. Read pairs that map to different contigs indicate
which contigs are from the same species.
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[00250] Example 5. Methods for producing extremely long-range
read pairs (XL.RPs)
[00251] Using commercially available kits, DNA is extracted to
fragments sizes up to 150 kbp. The DNA is assembled into a
reconstituted chromatin structure in vitro using a commercial kit
from Activ Motif. The chromatin is biotinylated, fixed with
formaldehyde, and immobilized onto streptavidin beads. The DNA
fragments are digested with a restriction enzyme and incubated
overnight. The resulting sticky ends are filled-in with an alpha-
thio-dGTP and a biotinylated dCTP to generate blunt ends. The blunt
ends are ligated with T4 ligase. The reconstituted chromatin is
digested with a proteinase to recover the ligated DNA. The DNA is
extracted from the beads and subject to an exonuclease digestion to
remove biotin from unligated ends. The DNA recovered is sheared and
the ends are filled-in with dNTPs. The biotinylated fragments are
purified by a pull-down with streptavidin beads. In some cases,
adaptors are ligated and the fragments are PCT amplified for high-
throughput Sequencing.
[00252] Example 6. Methods for producing a high quality human
genome assembly
[00253] With the knowledge that read pairs spanning considerable
genomic distances can be generated by the disclosure, the
utilization of this information for genomic assembly can be tested.
The disclosure can significantly improve the linkage of de novo
assemblies, potentially to chromosome-length scaffolds. An
assessment can be performed on how complete an assembly can be
produced and how much data will be required using the disclosure.
To evaluate the efficacy of the present method for producing data
that is valuable for assembly, a standard Illumina shotgun library
and XLRP libraries can be built and sequenced. In one case, data
from 1 Illumina HiSeq lane each of a standard shotgun library and
an XLRP library are used. The data generated from each method is
tested and compared with various existing assemblers. Optionally, a
new assembler is also written to specifically tailor to the unique
data produced by the disclosure. Optionally, a well-characterized
human sample is used to provide a reference to compare the assembly
produced by the present method against to assess its accuracy and
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completeness. Using the knowledge gained in the previous analyses,
an assembler is produced to increase efficient and effective
utilization the XLRP and shotgun data. A genome assembly of the
quality of the December 2002 mouse genome draft, or better is
generated using methods described herein.
[00254] One sample that can be used for this analysis is
NA12878. DNA from sample cells are extracted using a variety of
published techniques designed to maximize DNA fragment length. A
standard Illumina TruSeq shotgun library and an XLRP library are
each built. A single HiSeq lane of 2x150 bp sequence is obtained
for each library, which may yield approximately 150 million read
pairs per library. The shotgun data are assembled into contigs
using algorithms for whole genome assembly. Examples of such
algorithms include: Meraculous as described in Chapman et al. (PLOS
ONE 6(8):e2350 (2011)) or SGA as described in Simpson et al.
(Genome research 22(3):549-56 (2012)). The XLRP library reads are
aligned to the contigs produced by the initial assembly. The
alignments are used to further link the contigs. Once the
effectiveness of the XLRP library for connecting contigs is
ascertained, the Meraculous assembly is extended to integrate both
the shotgun and XLRP libraries simultaneously into a single
assembly process. Meraculous provides a strong foundation for the
assembler. Optionally, an all-in-one assembler is produced to suit
the specific needs of the disclosure. The human genome assembled by
the disclosure is compared to any known sequence to evaluate the
quality in the assembly of the genome.
[00255] Example 7. Methods for phasing of heterozygous SNPs for
a human sample at high accuracy from a small data set
[00256] In one experiment, approximately 44% of the heterozygous
variants in a test human sample dataset are phased. All or nearly
all phasing variants that are within one read-length's distance of
a restriction site are captured. By using in silica analysis, more
variants for phasing can be captured by using longer read lengths
and using one or more combinations restriction enzymes for
digestion. Using a combination of restriction enzymes with
different restriction sites increases the proportion of the genome
(and therefore heterozygous sites) that is within range of one of
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the two restriction sites that participate in each read pair. In
silica analysis shows that the methods of the disclosure can phase
more than 95% of known heterozygous positions using various
combinations of two restriction enzymes. Additional enzymes and
greater read lengths further increase the fraction of heterozygous
sites that are observed and phased, up to a complete coverage and
phasing.
[00257] Heterozygous site coverages achievable with various
combinations of two restriction enzymes are calculated. The top
three combinations, in terms of heterozygous sites in read
proximity, are tested with the protocol. For each of these
combinations, an XLRP library is produced and sequenced. The
resulting reads are aligned to a human reference genome and
compared to the known haplotypes of the sample to determine the
accuracy of the protocol. Up to 90% or more of the heterozygous
SNPs for a human sample are phased at an accuracy of 99% or greater
using only 1 lane of Illumina HiSeq data. In addition, further
variants are captured by increasing the read length to 300 bp. The
read area around the observable restriction sites is effectively
doubled. Additional restriction enzyme combinations are implemented
increasing the coverage and accuracy.
[00258] Example 8. Extraction and effects of high molecular
weight DNA:
[00259] DNA up to 150 kbp was extracted with commercially
available kits. FIG. 7 demonstrates that XLRP libraries can be
generated from capture read pairs up to maximum fragment lengths of
the extracted DNA. Accordingly, the methods disclosed herein can be
expected to be capable of generating read pairs from even longer
stretches of DNA. There are numerous well-developed processes for
high molecular weight DNA recovery, and these methods can be used
with the methods or protocols disclose herein. Using an extraction
method to produce large fragment lengths of DNA, an XLRP library is
created from these fragments and the read pairs that are produced
can be evaluated. For example, large molecular weight DNA can be
extracted by, (1) gentle lysis of the cells according to Teague et
al. (Proc. Nat. Acad. Sci. USA 107(24): 10848-53 (2010)) or Zhou et
al. (PLOS Genetics, 5(11):e1000711 (2009)); and (2) agarose gel
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plugs according to Wing et al. (The Plant Journal: for Cell and
Molecular Biology, 4(5):893-8 (1993)).
These
methods are capable of generating long DNA fragments beyond what is
routinely required for next generation sequencing; however, any
other suitable methods known in the art can be substituted for
achieving similar results. The Aurora System provides exceptional
results and can separate and concentrate DNA from tissue or other
preparations up to, and beyond, a megabase in length. DNA
extractions are prepared using each of these methodologies,
beginning from a single GM12878 cell culture to control for
possible differences at the sample level. The size distribution of
the fragments can be evaluated by pulsed field gel electrophoresis
according to Herschleb et al. (Nature Protocols 2(3):677-84
(2007)). Using the foregoing methods, extremely large stretches of
DNA can be extracted and used to build XLRP libraries. The XLRP
library is then sequenced and aligned. The resulting read data are
analyzed by comparing the genomic distance between read pairs to
the fragment sizes observed from the gel.
[00260] Example 9. Reducing read-pairs from undesired genomic
regions,
[00261] RNA complementary to the undesired genomic regions is
produced by in vitro transcription and added to the reconstructed
chromatin prior to crosslinking. As the supplemented RNA binds to
one or more undesired genomic regions, RNA binding decreases the
crosslinking efficiency at these regions. The abundance of DNA from
these regions in the cross-linked complexes is thereby reduced. The
reconstructed chromatin is biotinylated and immobilized, and used
as described above. In some cases, the RNA is designed to target
repetitive regions in the genome.
[00262] Example 10. Increasing read-pairs from desired chromatin
regions
[00263] DNA from desired chromatin regions is produced in
double stranded form for gene assembly or haplotyping.
Representation of DNA from undesired regions is accordingly
reduced. Double-stranded DNA from desired chromatin regions is
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generated by primers that tile at such regions in multi-kilobase
intervals. In other implementations of the method, the tiling
intervals are varied to address desired regions of different sizes
with desired replication efficiency. Primer binding sites across
the desired regions are contacted with primers, optionally by
melting the DNA. New strands of DNA are synthesized using the
tiled primers. Undesired regions are reduced or eliminated, for
example by targeting these regions with an endonuclease specific to
single-stranded DNA. The remaining desired regions can be
optionally amplified. The prepared sample is subjected to the
sequencing library preparation methods as described elsewhere
herein. In some implementations, read-pairs spanning distances up
to the length of each desired chromatin regions are generated from
each such desired chromatin region.
[00264] While preferred embodiments of the disclosure have been
shown and described herein, it will be obvious to those skilled in
the art that such embodiments are provided by way of example only.
Numerous variations, changes, and substitutions will now occur to
those skilled in the art without departing from the disclosure. It
should be understood that various alternatives to the embodiments
of the disclosure described herein may be employed in practicing
the disclosure. It is intended that the following claims define
the scope of the disclosure and that methods and structures within
the scope of these claims and their equivalents be covered thereby.
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